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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-11-11</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001213037</issuerCik>
        <issuerName>Trovagene, Inc.</issuerName>
        <issuerTradingSymbol>TROV</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001166309</rptOwnerCik>
            <rptOwnerName>BRIDGER MANAGEMENT, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>90 PARK AVENUE, 40TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10016</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <officerTitle></officerTitle>
            <otherText>Former 10% Owner</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001258394</rptOwnerCik>
            <rptOwnerName>MIGNONE ROBERTO</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>90 PARK AVENUE, 40TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10016</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, $.0001 par value per share</value>
            </securityTitle>
            <transactionDate>
                <value>2016-11-11</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>322472</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>3.08</value>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2968115</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See footnotes</value>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">The price reported in Column 4 is a weighted average price, rounded to the nearest whole cent. These Shares (as defined below) were sold in multiple transactions at prices ranging from $3.00 to $3.38, inclusive. The Reporting Persons undertake to provide to the Issuer, any security holder of the Issuer, or the staff of the Securities and Exchange Commission, full information regarding the number of Shares sold at each separate price within the ranges set forth in footnote (1) to this Form 4.</footnote>
        <footnote id="F2">The shares of Common Stock, $.0001 par value per share (the &quot;Shares&quot;), reported herein as indirectly beneficially owned by the Reporting Persons are held of record by Swiftcurrent Partners, L.P., Swiftcurrent Offshore Master Ltd. and Bridger Healthcare Ltd.  Bridger Management LLC is the investment adviser to Swiftcurrent Partners L.P., Swiftcurrent Offshore Master Ltd., and Bridger Healthcare Ltd., and as such, may be deemed to share beneficial ownership of the Shares. Roberto Mignone is the manager of Bridger Management, LLC.</footnote>
        <footnote id="F3">Each reporting person and entity named herein disclaims beneficial ownership of the reported securities except to the extent  of his or its pecuniary interest therein and this report shall not be deemed an admission that the reporting person or any  entity named herein is the beneficial owner of the securities for purposes of Section 16, or for any other purpose.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Roberto Mignone, Manager of Bridger Management, LLC</signatureName>
        <signatureDate>2016-11-15</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Roberto Mignone</signatureName>
        <signatureDate>2016-11-15</signatureDate>
    </ownerSignature>
</ownershipDocument>
