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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2016-01-10</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001484565</issuerCik>
        <issuerName>Capnia, Inc.</issuerName>
        <issuerTradingSymbol>CAPN</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001614821</rptOwnerCik>
            <rptOwnerName>Anish Bhatnagar</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1235 RADIO ROAD, SUITE 110</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>REDWOOD CITY</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94065</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.61</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2016-01-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>300000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2016-01-10</value>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
                <footnoteId id="F4"/>
                <footnoteId id="F5"/>
                <footnoteId id="F6"/>
                <footnoteId id="F7"/>
            </exerciseDate>
            <expirationDate>
                <value>2026-01-10</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>300000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>300000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">One forty-eighth (1/48) of the total number of shares subject to the Option shall vest each month following January 10, 2016 (the &quot;Vesting Commencement Date&quot;) on the same day of the month as the Vesting Commencement Date (and if there is no corresponding day, on the last day of the month), such that all of the shares subject to the Option will have vested as of the fourth anniversary of the Vesting Commencement Date, subject to Participant continuing to be a Service Provider (as defined in the Plan) through each such date; provided, however, that if a termination without &quot;Cause&quot; or resignation for &quot;Good Reason&quot; by Participant occurs before six (6) months prior to a Change in Control of the Company,</footnote>
        <footnote id="F2">(Continued from Footnote 1) then twenty-five percent (25%) of any unvested equity awards held by Participant as of the date of such termination without cause or resignation for good reason shall immediately vest and become fully exercisable; provided, further, that if termination without &quot;Cause&quot; or resignation for &quot;Good Reason&quot; by Participant occurs within six (6) months prior to, or twelve (12) months following, a Change in Control of the Company, then one hundred percent (100%) of any unvested equity awards held by Participant as of the date of such termination without &quot;Cause&quot; or resignation for &quot;Good Reason&quot; shall immediately vest and become fully exercisable; provided, further that following termination without &quot;Cause&quot; or resignation for &quot;Good Reason&quot; by Participant at any time, then Participant shall have one year to exercise any vested options.</footnote>
        <footnote id="F3">(Continued from Footnote 2) &quot;Cause&quot; means: (i) Participant's act of personal dishonesty in connection with his responsibilities as an employee that is intended to result in Participant's substantial personal enrichment; (ii) Participant being convicted of, or pleading no contest or guilty to, (x) a misdemeanor that the Company reasonably believes has had or will have a material detrimental effect on the Company, or (y) any felony; (iii) Participant's gross misconduct; (iv) Participant's willful and continued failure to perform the duties and responsibilities of Participant's position after there has been delivered to Participant a written demand for performance from the Company that describes the basis for the Company's belief that Participant has not substantially performed Participant's duties and Participant has not corrected such failure within thirty (30) days of such written demand;</footnote>
        <footnote id="F4">(Continued from Footnote 3) or (v) Participant's material violation of any written Company employment policy or standard of conduct, including a material breach of the Participant's confidential information agreement.</footnote>
        <footnote id="F5">(Continued from Footnote 4) &quot;Good Reason&quot; means Participant's resignation within thirty (30) days following the expiration of any Company cure period (discussed below) following the occurrence of one or more of the following, without Participant's consent: (i) a material reduction in Participant's Base Salary, excluding the substitution of substantially equivalent compensation and benefits, that is not generally applicable to all Company senior management or employees of the Company generally; (ii) a material reduction of Participant's authority, duties or responsibilities, unless Participant is provided with a comparable position; provided, however, that a reduction in authority, duties, or responsibilities solely by virtue of the Company being acquired and made part of a larger entity whether as a subsidiary,</footnote>
        <footnote id="F6">(Continued from Footnote 5) business unit or otherwise (as, for example, when the Chief Executive Officer of the Company remains as such following an acquisition where the Company becomes a wholly owned subsidiary of the acquirer, but is not made the Chief Executive Officer of the acquiring corporation) will not constitute &quot;Good Reason&quot;; or (iii) a material change in the geographic location of Participant's primary work facility or location; provided, that a relocation of fifty (50) miles or less from Participant's then present location or to Participant's home as Participant's primary work location will not be considered a material change in geographic location.</footnote>
        <footnote id="F7">(Continued from Footnote 6) In order for an event to qualify as Good Reason, Participant must not terminate employment with the Company without first providing the Company with written notice of the acts or omissions constituting the grounds for &quot;Good Reason&quot; within ninety (90) days of the initial existence of the grounds for &quot;Good Reason&quot; and a reasonable cure period of not less than thirty (30) days following the date of such notice, and such grounds must not have been cured during such time..</footnote>
    </footnotes>

    <remarks>President and Chief Executive Officer</remarks>

    <ownerSignature>
        <signatureName>/s/ David D. O'Toole, As Attorney-in Fact</signatureName>
        <signatureDate>2016-01-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
