<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0206</schemaVersion>

    <documentType>3/A</documentType>

    <periodOfReport>2016-05-25</periodOfReport>

    <dateOfOriginalSubmission>2016-05-25</dateOfOriginalSubmission>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001657197</issuerCik>
        <issuerName>Cotiviti Holdings, Inc.</issuerName>
        <issuerTradingSymbol>COTV</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001673364</rptOwnerCik>
            <rptOwnerName>Alexander Elizabeth Connolly</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O COTIVITI HOLDINGS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>115 PERIMETER CENTER PLACE, SUITE 700</rptOwnerStreet2>
            <rptOwnerCity>ATLANTA,</rptOwnerCity>
            <rptOwnerState>GA</rptOwnerState>
            <rptOwnerZipCode>30346</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Options (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.26</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2023-12-22</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, par value $0.001 per share</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>97600</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These options have vested and are immediately exercisable.</footnote>
        <footnote id="F2">The footnote in the Reporting Person's original Form 3 incorrectly described the vesting schedule for the Reporting Person's options.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Jonathan Olefson, attorney-in-fact</signatureName>
        <signatureDate>2016-06-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
