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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2007-06-29</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000745788</issuerCik>
        <issuerName>VioQuest Pharmaceuticals, Inc.</issuerName>
        <issuerTradingSymbol>VQPH</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001208492</rptOwnerCik>
            <rptOwnerName>GREENLEAF DANIEL E</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>180 MT. AIRY ROAD, SUITE 102</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BASKING RIDGE</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>07920</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>President and CEO</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock, $.001 par value</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>80000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.88</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-02-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, $.001 par value</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>891396</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>891396</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options</value>
                <footnoteId id="F3"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.89</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-10-19</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, $.001 par value</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1445080</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1445080</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Stock Options</value>
                <footnoteId id="F3"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.56</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-10-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, $.001 par value</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>394580</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>394580</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeTransaction>
            <securityTitle>
                <value>Senior Convertible Promissory Notes</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.38</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2007-06-29</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>46052</value>
                    <footnoteId id="F5"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F6"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2007-06-29</value>
            </exerciseDate>
            <expirationDate>
                <value>2009-06-29</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, $.01 par value</value>
                    <footnoteId id="F6"/>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>46052</value>
                    <footnoteId id="F5"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>46052</value>
                    <footnoteId id="F5"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>.40</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2007-06-29</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>11513</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F6"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2007-06-29</value>
            </exerciseDate>
            <expirationDate>
                <value>2012-06-29</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock, $.01 par value</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11513</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>11513</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">297,132 shares vest on each of 2/1/06, 2/1/07 and 2/1/08.</footnote>
        <footnote id="F2">481,693 shares vest on each of 02/01/06 and 02/01/07 and 481,694 shares vest on 02/01/08.</footnote>
        <footnote id="F3">Issued in accordance with Mr. Greenleaf's employment agreement dated 2/1/2005, which requires additional stock options to be issued to maintain Mr. Greenleaf's aggregate stock options to be equal to 5% of the Company's outstanding common stock until certain events occur.</footnote>
        <footnote id="F4">197,290 shares vest on each of 2/1/07 and 2/1/08.</footnote>
        <footnote id="F5">Reflects the number of shares to be acquired under a voluntary conversion.  Actual number and type of security under a mandatory conversion may vary.</footnote>
        <footnote id="F6">The Reporting Person invested $17,500 in a Convertible Note financing, whereby the Note is convertible (voluntarily) into shares of Common Stock or (by mandatory conversion) into Common Stock or another security.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>/s/ Daniel E. Greenleaf</signatureName>
        <signatureDate>2007-07-03</signatureDate>
    </ownerSignature>
</ownershipDocument>
