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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2008-03-14</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000724606</issuerCik>
        <issuerName>PANERA BREAD CO</issuerName>
        <issuerTradingSymbol>PNRA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001423667</rptOwnerCik>
            <rptOwnerName>Blair Scott G</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>THREE CHARLES RIVER STREET</rptOwnerStreet1>
            <rptOwnerStreet2>63 KENDRICK STREET</rptOwnerStreet2>
            <rptOwnerCity>NEEDHAM</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02494</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>SVP, Chief Legal Officer, Sec.</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Class A Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-03-14</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1084</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4738</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Class A Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2008-03-14</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>542</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5280</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Employee Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>40.35</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-03-14</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2168</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-03-14</value>
                <footnoteId id="F4"/>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>2168</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>2168</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Choice Award (Right to Buy Class A Common Stock)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <footnoteId id="F5"/>
                <footnoteId id="F6"/>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2008-03-14</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>0</value>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2008-03-14</value>
            </exerciseDate>
            <expirationDate>
                <value>2008-03-28</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Class A Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                    <footnoteId id="F5"/>
                    <footnoteId id="F6"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Represents award of restricted shares of Class A common stock, par value $0.0001 per share (&quot;Class A Common Stock&quot;), under the Company's 2005 Long Term Incentive Progam, as amended (the &quot;LTIP&quot;), and the Company's 2006 Stock Incentive Plan (the &quot;2006 Plan&quot;).</footnote>
        <footnote id="F2">Represents grant of restricted shares of Class A Common Stock the Reporting Person elected to receive under a Choice Award granted pursuant to the LTIP.</footnote>
        <footnote id="F3">Represents grant of option to purchase Class A Common Stock that the Reporting Person elected to receive under a Choice Award granted pursuant to the LTIP.  The stock options vest over a five-year period from the date of grant, with 25% vesting on the second anniversary of the date of grant, and an additional 25% vesting on the third, fourth and fifth anniversaries, respectively.</footnote>
        <footnote id="F4">The options terminate six (6) years from the date of grant, but are subject to earlier termination as provided in the award agreement, the LTIP and the 2006 Plan.</footnote>
        <footnote id="F5">Represents a choice award under the 2006 Plan, permitting the Reporting Person to elect to receive, effective March 28, 2008, unless otherwise determined by the Compensation and Stock Option Committee of the Board of Directors (the &quot;Compensation Committee&quot;), an award in the form of (i) up to a number of shares of Class A Common Stock, as has a fair market value of $100,000 on March 28, 2008 as determined by the closing price of shares of Class A Common Stock on The Nasdaq Global Market on that date, or (ii) stock options to purchase up to a number of shares of Class A Common Stock as would cause the stock option to have a fair market value of $100,000 on March 28, 2008 based on the Black-Scholes option pricing model, or (iii) a combination of restricted stock and stock options (in 25% increments).</footnote>
        <footnote id="F6">The options would have an exercise price equal to the closing price of the Class A Common Stock on The Nasdaq Global Market on March 28, 2008, unless otherwise determined by the Compensation Committee, and vest over a three (3) year period from the date of grant, with 33 1/3% vesting annually.  The options covered by the agreement will terminate six (6) years from the date of the agreement, but will be subject to earlier termination as provided in the award agreement or the 2006 Plan.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Scott G. Blair</signatureName>
        <signatureDate>2008-03-18</signatureDate>
    </ownerSignature>
</ownershipDocument>
