In a fuel cell system including a fuel cell supplied with reaction gases for generating an electric power, and a combustion heater supplied with the reaction gases for heating the fuel cell during warming-up, an electric discharging circuit is provided to discharge an electric current from the fuel cell supplied with the reaction gases to decrease a voltage difference applied to the membrane sandwiched between the anode and cathode during the warming-up. The combustion heater is connected in series or in parallel with the fuel cell system.