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<!-- DFIN ActiveDisclosure(SM) XBRL Schema Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date      : 2022-02-28T20:30:01.3110248+00:00 -->
<!-- Version            : 5.0.1.728 -->
<!-- Package ID         : 7d376a06224b4ca7b772db77067093a0 -->
<!-- Copyright (c) 2022 Donnelley Financial Solutions, Inc. All Rights Reserved. -->
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  <xsd:element id="apls_ProceedsFromPaymentsForDevelopmentDerivativeLiability" name="ProceedsFromPaymentsForDevelopmentDerivativeLiability" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_PaymentsForCappedCallTransactionsAndAssociatedCosts" name="PaymentsForCappedCallTransactionsAndAssociatedCosts" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ProceedsFromIssuanceOfConvertibleNotesNetOfIssuanceCosts" name="ProceedsFromIssuanceOfConvertibleNotesNetOfIssuanceCosts" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_ProceedsFromStockOptionsAndWarrantsExercised" name="ProceedsFromStockOptionsAndWarrantsExercised" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_EquityComponentOfConvertibleNotes" name="EquityComponentOfConvertibleNotes" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ProductRevenuesAccountsReceivableAndReservesForProductSalesTextBlock" name="ProductRevenuesAccountsReceivableAndReservesForProductSalesTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ProductRevenuesAccountsReceivableAndReservesForProductSalesAbstract" name="ProductRevenuesAccountsReceivableAndReservesForProductSalesAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilityDisclosureTextBlock" name="DevelopmentDerivativeLiabilityDisclosureTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_AccruedExpensesAndPrepaidAssetsTextBlock" name="AccruedExpensesAndPrepaidAssetsTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_AccruedExpensesAndPrepaidAssetsAbstract" name="AccruedExpensesAndPrepaidAssetsAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ProductRevenuesPolicyPolicyTextBlock" name="ProductRevenuesPolicyPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_OfferingCostsPolicyTextBlock" name="OfferingCostsPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilityAndDevelopmentLiabilityPolicyTextBlock" name="DevelopmentDerivativeLiabilityAndDevelopmentLiabilityPolicyTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_SummaryOfCommonStockReservedForFutureIssuanceTableTextBlock" name="SummaryOfCommonStockReservedForFutureIssuanceTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_SummaryOfDevelopmentDerivativeLiabilityTableTextBlock" name="SummaryOfDevelopmentDerivativeLiabilityTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_SupplementalCashFlowInformationRelatedToOperatingLeasesTableTextBlock" name="SupplementalCashFlowInformationRelatedToOperatingLeasesTableTextBlock" type="dtr-types:textBlockItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_NatureOfOrganizationAndOperationsLineItems" name="NatureOfOrganizationAndOperationsLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_NatureOfOrganizationAndOperationsTable" name="NatureOfOrganizationAndOperationsTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_CollaborationAndLicenseAgreementMember" name="CollaborationAndLicenseAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_SwedishOrphanBiovitrumABPublMember" name="SwedishOrphanBiovitrumABPublMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwoThousandNineteenAndTwoThousandTwentyConvertibleNotesMember" name="TwoThousandNineteenAndTwoThousandTwentyConvertibleNotesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ConvertibleSeniorNotesDueTwoThousandTwentySixMember" name="ConvertibleSeniorNotesDueTwoThousandTwentySixMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ExchangeAgreementsMember" name="ExchangeAgreementsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_CappedCallTransactionMember" name="CappedCallTransactionMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_FollowOnPublicOfferingsMember" name="FollowOnPublicOfferingsMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_AggregateMilestonePaymentsUponAchievementOfSpecifiedOneTimeRegulatoryAndCommercialMilestoneEvents" name="AggregateMilestonePaymentsUponAchievementOfSpecifiedOneTimeRegulatoryAndCommercialMilestoneEvents" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DevelopmentCostReimbursement" name="DevelopmentCostReimbursement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_RoyaltiesEntitledToReceiveAfterFirstCommercialSaleOfApplicableLicensedProductPeriod" name="RoyaltiesEntitledToReceiveAfterFirstCommercialSaleOfApplicableLicensedProductPeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_UpfrontPayment" name="UpfrontPayment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DebtConversionConvertedInstrumentAdditionalSharesIssuedForSettlementOfDebtIssuanceCost" name="DebtConversionConvertedInstrumentAdditionalSharesIssuedForSettlementOfDebtIssuanceCost" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_DebtConversionConvertedInstrumentAdditionalSharesAgreedToIssueForSettlementOfDebtIssuanceCost" name="DebtConversionConvertedInstrumentAdditionalSharesAgreedToIssueForSettlementOfDebtIssuanceCost" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_DebtInstrumentNumberOfCounterparties" name="DebtInstrumentNumberOfCounterparties" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_DebtInstrumentConvertibleInitialConversionPrice" name="DebtInstrumentConvertibleInitialConversionPrice" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_CashAndCashEquivalentsAndMarketableSecurities" name="CashAndCashEquivalentsAndMarketableSecurities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ScheduleOfSummaryOfSignificantAccountingPoliciesLineItems" name="ScheduleOfSummaryOfSignificantAccountingPoliciesLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ScheduleOfSummaryOfSignificantAccountingPoliciesTable" name="ScheduleOfSummaryOfSignificantAccountingPoliciesTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_FoodAndDrugAdministrationMember" name="FoodAndDrugAdministrationMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_SFJAgreementMember" name="SFJAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ObsoleteInventory" name="ObsoleteInventory" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DevelopmentLiabilities" name="DevelopmentLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_PaymentMadeUnderAgreement" name="PaymentMadeUnderAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_ProductRevenuesAccountsReceivableAndReservesForProductSalesLineItems" name="ProductRevenuesAccountsReceivableAndReservesForProductSalesLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ProductRevenuesAccountsReceivableAndReservesForProductSalesTable" name="ProductRevenuesAccountsReceivableAndReservesForProductSalesTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_AccruedLiabilitiesCurrentMember" name="AccruedLiabilitiesCurrentMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ProductSalesReserves" name="ProductSalesReserves" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_TwoThousandSeventeenStockIncentivePlanMember" name="TwoThousandSeventeenStockIncentivePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwoThousandSeventeenEmployeeStockPurchasePlanMember" name="TwoThousandSeventeenEmployeeStockPurchasePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_AdditionalFundingAmountUponAchievementOfDevelopmentMilestones" name="AdditionalFundingAmountUponAchievementOfDevelopmentMilestones" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_NumberOfMilestonePayments" name="NumberOfMilestonePayments" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_DevelopmentFundingForMinimumPeriodOfOperatingExpense" name="DevelopmentFundingForMinimumPeriodOfOperatingExpense" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EuropeanMedicinesAgencyMember" name="EuropeanMedicinesAgencyMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_IncreaseInAdditionalFundingForDevelopmentCosts" name="IncreaseInAdditionalFundingForDevelopmentCosts" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_NumberOfAdditionalAnnualPayments" name="NumberOfAdditionalAnnualPayments" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_AggregateAmountOfAdditionalAnnualPayments" name="AggregateAmountOfAdditionalAnnualPayments" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilitiesGross" name="DevelopmentDerivativeLiabilitiesGross" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_MinimumPaymentOfAdditionalFundingAmount" name="MinimumPaymentOfAdditionalFundingAmount" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ReclassificationToDevelopmentLiability" name="ReclassificationToDevelopmentLiability" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ImpliedCostOfBorrowingDiscountRates" name="ImpliedCostOfBorrowingDiscountRates" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_FirstPaymentDueUnderAgreement" name="FirstPaymentDueUnderAgreement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilities" name="DevelopmentDerivativeLiabilities" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilitiesUnamortizedDiscount" name="DevelopmentDerivativeLiabilitiesUnamortizedDiscount" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilitiesInterestRateEffectivePercentage" name="DevelopmentDerivativeLiabilitiesInterestRateEffectivePercentage" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_AccruedResearchAndDevelopmentCurrent" name="AccruedResearchAndDevelopmentCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_AccruedCostOfResearchCollaborationsCurrent" name="AccruedCostOfResearchCollaborationsCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_AccruedLicenseFeesCurrent" name="AccruedLicenseFeesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_AccruedPayrollLiabilitiesCurrent" name="AccruedPayrollLiabilitiesCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_PrepaidResearchAndDevelopmentCostCurrent" name="PrepaidResearchAndDevelopmentCostCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_TwoThousandNineteenConvertibleNotesMember" name="TwoThousandNineteenConvertibleNotesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwoThousandTwentyConvertibleNotesMember" name="TwoThousandTwentyConvertibleNotesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_PriorToMarchFifteenTwoThousandAndTwentySixConvertibleMember" name="PriorToMarchFifteenTwoThousandAndTwentySixConvertibleMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_LiabilityComponentMember" name="LiabilityComponentMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_EquityComponentMember" name="EquityComponentMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwoThousandTwentyOneConvertibleNotesMember" name="TwoThousandTwentyOneConvertibleNotesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_PaymentOfConvertibleDebtDiscountsAndCommissions" name="PaymentOfConvertibleDebtDiscountsAndCommissions" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_PaymentOfConvertibleDebtOfferingExpenses" name="PaymentOfConvertibleDebtOfferingExpenses" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DebtInstrumentConvertibleThresholdTradingPricePerPrincipalAmount" name="DebtInstrumentConvertibleThresholdTradingPricePerPrincipalAmount" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DebtInstrumentConvertibleCarryingAmountOfLiabilityComponent" name="DebtInstrumentConvertibleCarryingAmountOfLiabilityComponent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DebtConversionConvertedInstrumentAdditionalSharesIssued" name="DebtConversionConvertedInstrumentAdditionalSharesIssued" type="xbrli:sharesItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_LossOnConversionOfDebtRelatedToAdditionalSharesIssued" name="LossOnConversionOfDebtRelatedToAdditionalSharesIssued" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_AdditionalAmountIssuedInPaymentOfIssuanceCosts" name="AdditionalAmountIssuedInPaymentOfIssuanceCosts" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_LossOnConversionsOfDebt" name="LossOnConversionsOfDebt" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DebtInstrumentConvertibleInitialConversionCapPrice" name="DebtInstrumentConvertibleInitialConversionCapPrice" type="dtr-types:perShareItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_PremiumPaidForCappedCallTransaction" name="PremiumPaidForCappedCallTransaction" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_LesseeOperatingLeaseMaximumTermOfOptionsToTerminateLease" name="LesseeOperatingLeaseMaximumTermOfOptionsToTerminateLease" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ConvertibleSeniorNotesNoncurrent" name="ConvertibleSeniorNotesNoncurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ConvertibleSeniorNotesMember" name="ConvertibleSeniorNotesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_DevelopmentDerivativeLiabilityMember" name="DevelopmentDerivativeLiabilityMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_MarketableSecuritiesMember" name="MarketableSecuritiesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_UniversityOfPennsylvaniaMember" name="UniversityOfPennsylvaniaMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwoThousandTenLicenseAgreementMember" name="TwoThousandTenLicenseAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_SobiAgreementAndAnotherLicensingTransactionMember" name="SobiAgreementAndAnotherLicensingTransactionMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ResearchCollaborationAgreementMember" name="ResearchCollaborationAgreementMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_BeamTherapeuticsIncorporationMember" name="BeamTherapeuticsIncorporationMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_NonRefundableUpfrontPayment" name="NonRefundableUpfrontPayment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ContractResearchAndDevelopmentReimbursementCommitment" name="ContractResearchAndDevelopmentReimbursementCommitment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ContraResearchAndDevelopmentExpense" name="ContraResearchAndDevelopmentExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_RevenueReversalOnBasisOfMilestoneAchievement" name="RevenueReversalOnBasisOfMilestoneAchievement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ContractResearchAndDevelopmentReceivable" name="ContractResearchAndDevelopmentReceivable" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_ContractResearchAndDevelopmentCurrent" name="ContractResearchAndDevelopmentCurrent" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_ContractResearchAndDevelopmentLongTermAssets" name="ContractResearchAndDevelopmentLongTermAssets" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_AnnualLicenseMaintenanceFees" name="AnnualLicenseMaintenanceFees" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_SalesMilestonePaymentsBasedOnAchievementOfAnnualSalesMilestones" name="SalesMilestonePaymentsBasedOnAchievementOfAnnualSalesMilestones" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_NumberOfLicensedProducts" name="NumberOfLicensedProducts" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_LicenseFees" name="LicenseFees" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DevelopmentMilestoneAchievement" name="DevelopmentMilestoneAchievement" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_SublicenseFeeOwed" name="SublicenseFeeOwed" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_CollaborativeArrangementTermOfAgreement" name="CollaborativeArrangementTermOfAgreement" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_CollaborativeArrangementNumberOfResearchPrograms" name="CollaborativeArrangementNumberOfResearchPrograms" type="xbrli:integerItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_CollaborativeArrangementUpfrontNonRefundableAmountPayable" name="CollaborativeArrangementUpfrontNonRefundableAmountPayable" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_CollaborativeArrangementUpFrontPaymentInNextTwelveMonths" name="CollaborativeArrangementUpFrontPaymentInNextTwelveMonths" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" />
  <xsd:element id="apls_CollaborativeArrangementMaximumExtendableTermOfAgreement" name="CollaborativeArrangementMaximumExtendableTermOfAgreement" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_DefinedContributionPlanEligibilityCriteriaMinimumAgeOfFullTimeEmployees" name="DefinedContributionPlanEligibilityCriteriaMinimumAgeOfFullTimeEmployees" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EffectiveIncomeTaxRateReconciliationIntellectualPropertyTransfer" name="EffectiveIncomeTaxRateReconciliationIntellectualPropertyTransfer" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EffectiveIncomeTaxRateReconciliationChangeInStateApportionment" name="EffectiveIncomeTaxRateReconciliationChangeInStateApportionment" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EffectiveIncomeTaxRateReconciliationLossOnDebtConversion" name="EffectiveIncomeTaxRateReconciliationLossOnDebtConversion" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EffectiveIncomeTaxRateReconciliationPermanentAndOther" name="EffectiveIncomeTaxRateReconciliationPermanentAndOther" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_DeferredTaxAssetsDeferredInterestExpense" name="DeferredTaxAssetsDeferredInterestExpense" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DeferredTaxAssetsOrphanDrugCredits" name="DeferredTaxAssetsOrphanDrugCredits" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DeferredTaxAssetsConvertibleDebt" name="DeferredTaxAssetsConvertibleDebt" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DeferredTaxAssetLeaseLiability" name="DeferredTaxAssetLeaseLiability" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_DeferredTaxLiabilityRightOfUseAsset" name="DeferredTaxLiabilityRightOfUseAsset" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_DeferredTaxLiabilitiesSection481AAdjustment" name="DeferredTaxLiabilitiesSection481AAdjustment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_NetDeferredTaxAssetsBeforeValuationAllowance" name="NetDeferredTaxAssetsBeforeValuationAllowance" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_IncomeTaxesLineItems" name="IncomeTaxesLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_IncomeTaxesTable" name="IncomeTaxesTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_DeferredTaxAssetsTaxCreditCarryforwardsResearchAndDevelopment" name="DeferredTaxAssetsTaxCreditCarryforwardsResearchAndDevelopment" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_NetOperatingLossCarryforwardExpirationYear" name="NetOperatingLossCarryforwardExpirationYear" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ResearchAndDevelopmentTaxCreditCarryforwardExpirationYear" name="ResearchAndDevelopmentTaxCreditCarryforwardExpirationYear" type="xbrli:gYearItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_NetOperatingLossCarryforwardPeriod" name="NetOperatingLossCarryforwardPeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EstimatedTerminationCostsAndOtherFees" name="EstimatedTerminationCostsAndOtherFees" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_CommitmentsAndContingenciesLineItems" name="CommitmentsAndContingenciesLineItems" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_CommitmentsAndContingenciesTable" name="CommitmentsAndContingenciesTable" type="xbrli:stringItemType" substitutionGroup="xbrldt:hypercubeItem" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_BachemMember" name="BachemMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_NonCancellablePurchaseObligationSubstanceOverPeriod" name="NonCancellablePurchaseObligationSubstanceOverPeriod" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardExercisePriceFairValueOfCommonStockPercent" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardExercisePriceFairValueOfCommonStockPercent" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EquityIncentivePlanTwoThousandAndTenMember" name="EquityIncentivePlanTwoThousandAndTenMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwoThousandTwentyInducementStockIncentivePlanMember" name="TwoThousandTwentyInducementStockIncentivePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_TwentySeventeenEmployeeStockPurchasePlanMember" name="TwentySeventeenEmployeeStockPurchasePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ShareBasedCompensationAwardTrancheFourMember" name="ShareBasedCompensationAwardTrancheFourMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_EmployeeStockPurchasePlanMember" name="EmployeeStockPurchasePlanMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_CommonStockIssuanceDescription" name="CommonStockIssuanceDescription" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsAbstract" name="EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantInPeriodWeightedAverageRemainingContractualTerm" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantInPeriodWeightedAverageRemainingContractualTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisedInPeriodWeightedAverageRemainingContractualTerm" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisedInPeriodWeightedAverageRemainingContractualTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForefeitedInPeriodWeightedAverageRemainingContractualTerm" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForefeitedInPeriodWeightedAverageRemainingContractualTerm" type="xbrli:durationItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantInPeriodIntrinsicValue" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantInPeriodIntrinsicValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeitedInPeriodIntrinsicValue" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsForfeitedInPeriodIntrinsicValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisedInPeriodAggregateIntrinsicValue" name="ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisedInPeriodAggregateIntrinsicValue" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="instant" nillable="true" abstract="false" xbrli:balance="debit" />
  <xsd:element id="apls_PercentageOfEarningsWithheldToPurchaseSharesOfCommonStock" name="PercentageOfEarningsWithheldToPurchaseSharesOfCommonStock" type="dtr-types:percentItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" />
  <xsd:element id="apls_CashReceivedFromIssuanceOfPurchaseRights" name="CashReceivedFromIssuanceOfPurchaseRights" type="xbrli:monetaryItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="false" xbrli:balance="credit" />
  <xsd:element id="apls_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAbstract" name="ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAbstract" type="xbrli:stringItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
  <xsd:element id="apls_ConvertibleNotesMember" name="ConvertibleNotesMember" type="dtr-types:domainItemType" substitutionGroup="xbrli:item" xbrli:periodType="duration" nillable="true" abstract="true" />
</xsd:schema>
