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

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2011-06-10</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001317872</issuerCik>
        <issuerName>TomoTherapy Inc</issuerName>
        <issuerTradingSymbol>TOMO</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001396084</rptOwnerCik>
            <rptOwnerName>Robertson A Frederick</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1240 DEMING WAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>MADISON</rptOwnerCity>
            <rptOwnerState>WI</rptOwnerState>
            <rptOwnerZipCode>53717</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>CEO, President and Director</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2011-06-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1679472</value>
                </transactionShares>
                <transactionPricePerShare>
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                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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                    <value>0</value>
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                <value>Common Stock</value>
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            <transactionDate>
                <value>2011-06-10</value>
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            <deemedExecutionDate></deemedExecutionDate>
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                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
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                <transactionShares>
                    <value>475951</value>
                </transactionShares>
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                    <value>D</value>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By Robertson Revocable Trust</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.75</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2011-06-10</value>
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            <deemedExecutionDate></deemedExecutionDate>
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                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
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            <transactionTimeliness>
                <value></value>
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                <transactionShares>
                    <value>121186</value>
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                <transactionPricePerShare>
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                <transactionAcquiredDisposedCode>
                    <value>D</value>
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            <exerciseDate>
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            <expirationDate>
                <value>2012-12-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>121186</value>
                </underlyingSecurityShares>
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                    <value>D</value>
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        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option (right to buy)</value>
            </securityTitle>
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                <value>6.75</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2011-06-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
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                <transactionCode>D</transactionCode>
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            <transactionTimeliness>
                <value></value>
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            <transactionAmounts>
                <transactionShares>
                    <value>14814</value>
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                <transactionPricePerShare>
                    <footnoteId id="F4"/>
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                    <value>D</value>
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                <footnoteId id="F4"/>
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            <expirationDate>
                <value>2012-12-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>14814</value>
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            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
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        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Disposed of pursuant to the Agreement and Plan of Merger dated as of March 6, 2011 (the &quot;Merger Agreement&quot;) among Accuray Incorporated (&quot;Accuray&quot;), Jaguar Acquisition, Inc. and TomoTherapy Incorporated (&quot;TomoTherapy&quot;), in exchange for a combination of $5,290,336.80 in cash and 276,776 shares of Accuray common stock based on $3.15 per share and 0.1648 shares of Accuray Common Stock for each TomoTherapy share held.</footnote>
        <footnote id="F2">Disposed of pursuant to the Agreement and Plan of Merger dated as of March 6, 2011 (the &quot;Merger Agreement&quot;) among Accuray Incorporated (&quot;Accuray&quot;), Jaguar Acquisition, Inc. and TomoTherapy Incorporated (&quot;TomoTherapy&quot;), in exchange for a combination of $1,499,245.65 in cash and 78,436 shares of Accuray common stock based on $3.15 per share and 0.1648 shares of Accuray Common Stock for each TomoTherapy share held.</footnote>
        <footnote id="F3">These options vested over a three-year period with 68,000 shares vesting on 12/07/2008, 34,000 shares vesting on 12/07/2009 and 19,186 shares vesting on 12/07/2010. These stock options were cancelled and exchanged for 74,505 new stock options of Accuray with the same vesting terms, based on a conversion ratio of 0.6148, which is (A)(i) $3.15 divided by (ii) $7.00, the volume weighted average of the daily closing price of Accuray for the five (5) consecutive trading days preceding and including June 9, 2011, plus (B) 0.1648 pursuant to the Merger Agreement, at a new exercise price of $10.98, based on the previous exercise price divided by the same conversion ratio.</footnote>
        <footnote id="F4">These options vested on 12/07/2010. These stock options were cancelled and exchanged for 9,107 new stock options of Accuray with the same vesting terms, based on a conversion ratio of 0.6148, which is (A)(i) $3.15 divided by (ii) $7.00, the volume weighted average of the daily closing price of Accuray for the five (5) consecutive trading days preceding and including June 9, 2011, plus (B) 0.1648 pursuant to the Merger Agreement, at a new exercise price of $10.98, based on the previous exercise price divided by the same conversion ratio.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Frederick A. Robertson</signatureName>
        <signatureDate>2011-06-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
