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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-07-28</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001082526</issuerCik>
        <issuerName>SCIQUEST INC</issuerName>
        <issuerTradingSymbol>SQI</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001555454</rptOwnerCik>
            <rptOwnerName>Nelson Steven</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>3020 CARRINGTON MILL BLVD.</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 100</rptOwnerStreet2>
            <rptOwnerCity>MORRISVILLE</rptOwnerCity>
            <rptOwnerState>NC</rptOwnerState>
            <rptOwnerZipCode>27560</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2016-07-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8269</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>17.75</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Stock Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-07-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>7385</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F3"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>7385</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Stock Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-07-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1505</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F4"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F4"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1505</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Stock Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-07-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2085</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F5"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F5"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F5"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2085</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Stock Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-07-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>3169</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F6"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F6"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F6"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>3169</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Restricted Stock Unit</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F2"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-07-28</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>8481</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F7"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <footnoteId id="F7"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>8481</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Disposed of pursuant to the Merger Agreement.</footnote>
        <footnote id="F2">The restricted stock units convert into the right to receive an amount in cash equal to the product of (i) the total number of shares subject to such restricted stock unit and (ii) the per share merger consideration, less applicable taxes required to be withheld with respect to such payment.</footnote>
        <footnote id="F3">On July 31, 2012, the reporting person was granted 8,895 restricted stock units, vesting on July 31, 2013.  Once vested, (i) 1,510 of the shares of common stock subject to this restricted stock unit were immediately issued and (ii) the remaining 7,385 of the shares subject to this restricted stock unit were to be issued upon the termination of the reporting person's service on the Board of Directors. Pursuant to the Merger Agreement, the remaining restricted stock units were cancelled in exchange for a cash payment of $131,083.75, which represents the product of (i) the aggregate number of remaining shares of common stock subject to such restricted stock units (7,385 shares) and (ii) the merger consideration of $17.75 per share, with such cash payment subject to any required withholding of taxes.</footnote>
        <footnote id="F4">On April 24, 2013, the reporting person was granted 3,010 restricted stock units, vesting on April 24, 2014.  Once vested, (i) 50% of the shares of common stock subject to this restricted stock unit were immediately issued and (ii) 50% of the shares subject to this restricted stock unit were to be issued upon the termination of the reporting person's service on the Board of Directors. Pursuant to the Merger Agreement, the remaining restricted stock units were cancelled in exchange for a cash payment of $26,713.75, which represents the product of (i) the aggregate number of remaining shares of common stock subject to such restricted stock units (1,505 shares) and (ii) the merger consideration of $17.75 per share, with such cash payment subject to any required withholding of taxes.</footnote>
        <footnote id="F5">On April 30, 2014, the reporting person was granted 4,170 restricted stock units, vesting on April 30, 2015.  Once vested, (i) 50% of the shares of common stock subject to this restricted stock unit were immediately issued and (ii) 50% of the shares subject to this restricted stock unit were to be issued upon the termination of the reporting person's service on the Board of Directors. Pursuant to the Merger Agreement, the remaining restricted stock units were cancelled in exchange for a cash payment of $37,008.75, which represents the product of (i) the aggregate number of remaining shares of common stock subject to such restricted stock units (2,085 shares) and (ii) the merger consideration of $17.75 per share, with such cash payment subject to any required withholding of taxes.</footnote>
        <footnote id="F6">On April 29, 2015, the reporting person was granted 6,338 restricted stock units, vesting on April 29, 2016.  Once vested, (i) 50% of the shares of common stock subject to this restricted stock unit were immediately issued and (ii) 50% of the shares subject to this restricted stock unit were to be issued upon the termination of the reporting person's service on the Board of Directors. Pursuant to the Merger Agreement, the remaining restricted stock units were cancelled in exchange for a cash payment of $56,249.75, which represents the product of (i) the aggregate number of remaining shares of common stock subject to such restricted stock units (3,169 shares) and (ii) the merger consideration of $17.75 per share, with such cash payment subject to any required withholding of taxes.</footnote>
        <footnote id="F7">On April 27, 2016, the reporting person was granted 8,481 restricted stock units, vesting on April 27, 2017.  As the restricted stock units were not vested on July 28, 2016, the time of the Merger, the restricted stock units have been cancelled and forfeited for no consideration pursuant to the Merger Agreement.</footnote>
    </footnotes>

    <remarks>On July 28, 2016, the Issuer became a wholly owned subsidiary of SciQuest Parent, LLC (f/k/a AKKR Green Parent, LLC) pursuant to the merger (the &quot;Merger&quot;) effected in connection with that certain Agreement and Plan of Merger, dated May 30, 2016, by and among the Issuer, SciQuest Parent, LLC and AKKR Green Merger Sub, Inc. (the &quot;Merger Agreement&quot;).</remarks>

    <ownerSignature>
        <signatureName>/s/ Grant W. Collingsworth, attorney-in-fact for Steven Nelson</signatureName>
        <signatureDate>2016-07-29</signatureDate>
    </ownerSignature>
</ownershipDocument>
