A fuel cell system comprises a fuel cell; a reactive gas supply mechanism configured to supply a reactive gas to the fuel cell; a discharge flow path configured to discharge an off-gas and water discharged from the fuel cell; a valve provided in the discharge flow path; a remaining water purging controller configured to control a remaining water purging process of the fuel cell by using the reactive gas supply mechanism and the valve; a heating portion configured to heat the valve; and a failure detector configured to detect a failure of the heating portion. When a failure of the heating portion is detected, the remaining water purging controller performs the remaining water purging process and increases a water discharge power in the remaining water purging process than a water discharge power in the remaining water purging process performed when no failure of the heating portion is detected.