A fuel cell system having a fuel cell for causing reactant gas to be electrochemically reacted to generate power, a reactant gas supply path for supplying reactant gas to the fuel cell, a reactant gas recirculation path for recirculating exhaust gas discharged from the fuel cell and combining the recirculating exhaust gas with reactant gas flowing through the reactant gas supply path to the fuel cell, and a pump unit disposed in the reactant gas recirculation path to pump the recirculating exhaust gas through the reactant gas recirculation path. A pump-tempering apparatus increases the temperature of the pump unit and a controller controls the pump-tempering apparatus. After the controller receives a fuel cell system stop signal, the controller controls the pump-tempering apparatus such that the temperature of the pump unit becomes higher than the temperature of piping in the reactant gas recirculation path.