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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2017-01-27</periodOfReport>

    <dateOfOriginalSubmission>2017-01-31</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001590560</issuerCik>
        <issuerName>uniQure N.V.</issuerName>
        <issuerTradingSymbol>QURE</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001693830</rptOwnerCik>
            <rptOwnerName>Petry Harald</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O UNIQURE N.V.</rptOwnerStreet1>
            <rptOwnerStreet2>MEIBERGDREFF 61</rptOwnerStreet2>
            <rptOwnerCity>AMSTERDAM</rptOwnerCity>
            <rptOwnerState>P7</rptOwnerState>
            <rptOwnerZipCode>1005 BA</rptOwnerZipCode>
            <rptOwnerStateDescription>NETHERLANDS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Scientific Officer</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable></nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.37</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-01-27</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>43000</value>
                    <footnoteId id="F4"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2027-01-27</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Ordinary Shares</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>43000</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>43000</value>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Performance Share Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2017-01-27</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>43500</value>
                    <footnoteId id="F4"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2020-01-27</value>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Ordinary Shares</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>43500</value>
                    <footnoteId id="F4"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>43500</value>
                    <footnoteId id="F4"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The Stock Option vests 25% on January 27, 2018 and 6.25% quarterly thereafter until fully vested.</footnote>
        <footnote id="F2">Performance Shares Units of a maximum of 43,250 shares of the Company's Ordinary Shares were granted on January 27, 2017. The Board of Directors shall determine how many Performance Share Units are to be granted in conjunction with a review of certain performance goals associated with the grant. Any such Performance Share Units granted by the Board of Directors shall vest 100% on January 27, 2020.</footnote>
        <footnote id="F3">Expiration date is not applicable.</footnote>
        <footnote id="F4">Due to clerical error, the Form 4, as originally filed, incorrectly reports the number of options granted as 43,250 and the number of performance share units granted as 43,250. The Form 4, as amended by this Form 4/A, correctly reports such information.</footnote>
    </footnotes>

    <remarks>See Exhibit 24 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>Lauren M. Watson, Attorney-in-Fact</signatureName>
        <signatureDate>2017-02-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
