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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-08-13</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000932352</issuerCik>
        <issuerName>Urigen Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>URGP.OB</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000905011</rptOwnerCik>
            <rptOwnerName>GOLDBERG MICHAEL M</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O MONTAUR CAPITAL PARTNERS</rptOwnerStreet1>
            <rptOwnerStreet2>152 WEST 57TH STREET, 4TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</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>
        <derivativeTransaction>
            <securityTitle>
                <value>Convertible Note</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>202500</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2009-08-13</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>5</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>202500</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.10</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2009-08-13</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-10-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2025000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2025500</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See &quot;Explanation of Responses&quot;</value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The transaction is the acquisition of the Convertible Note by Platinum-Montaur Life Sciences, LLC directly from the Issuer.</footnote>
    </footnotes>

    <remarks>All of the equity derivative securities listed under Table II are owned directly and beneficially by Platinum-Montaur Life Sciences, LLC. Dr. Goldberg is a Managing Director of Platinum-Montaur Life Sciences, LLC and may be deemed to be a beneficial owner of such securities. Dr. Goldberg disclaims beneficial ownership of the equity derivative securities listed under Table II and the common stock issuable upon exercise or conversion of such equity derivative securities, except to the extent of his pecuniary interest in Platinum-Montaur Life Sciences, LLC. This report shall not be deemed an admission that Dr. Goldberg is the beneficial owner of these securities for purposes of Section 16 of the Securities Exchange act or 1934, as amended, or for any other purpose.

The Convertible Note provides a limitation on the conversion, such that the number of shares of Common Stock that may be acquired by the holder upon conversion shall be limited to the extent necessary to ensure that following such conversion, the total number of shares of Common Stock then beneficially owned does not exceed 4.99% and 9.99% of the total number of issued and outstanding shares of Common Stock.</remarks>

    <ownerSignature>
        <signatureName>Michael M. Goldberg</signatureName>
        <signatureDate>2009-08-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
