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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-03-02</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001183765</issuerCik>
        <issuerName>THRESHOLD PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>THLD</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001162183</rptOwnerCik>
            <rptOwnerName>MORGENTHALER PARTNERS VII LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>50 PUBLIC SQUARE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 2700</rptOwnerStreet2>
            <rptOwnerCity>CLEVELAND</rptOwnerCity>
            <rptOwnerState>OH</rptOwnerState>
            <rptOwnerZipCode>44113</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001316252</rptOwnerCik>
            <rptOwnerName>Christoffersen Ralph E</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>4430 ARAPAHOE AVENUE</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 200</rptOwnerStreet2>
            <rptOwnerCity>BOULDER</rptOwnerCity>
            <rptOwnerState>CO</rptOwnerState>
            <rptOwnerZipCode>80303</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>Former Director See Footnote 2</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-03-02</value>
            </transactionDate>
            <deemedExecutionDate>
                <value>2006-03-02</value>
            </deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1150000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>15.016</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1122345</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Distributed to the partners of Morgenthaler Partners VII, L.P.</footnote>
        <footnote id="F2">The shares are held by Morgenthaler Partners VII, LP (MPVII).  Ralph E. Christoffersen, was a director of Threshold Pharmaceuticals, Inc., until he resigned from the Board of Directors December 20, 2005, and is a Partner of Morgenthaler Management Partners VII, LLC (MMPVII), the managing partner of MPVII.  Dr. Christoffersen shares voting power over the shares with other members of MMPVII.  The natural persons who have voting or investment power over the shares held of record of MVPII are Robert C. Bellas, Jr., Greg E. Blonder, James W. Broderick, Ralph E. Christoffersen, Andrew S. Lanza, Theodore A. Laufik, Paul H. Levine, Gary R. Little, John D. Lutsi, Gary J. Morgenthaler, Robert D. Pavey, G. Gary Shaffer and Peter G. Taft.  Dr. Christoffersen disclaims beneficial ownership of the shares held by MPVII except to the extend of his pecuniary interest therein.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Theodore A. Laufik</signatureName>
        <signatureDate>2006-03-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
