The fuel cell system is equipped with a fuel cell for generating power by a reaction of fuel and oxidizer gases, a fuel gas flow passage for passing the fuel gas, an oxidizer gas flow passage for passing the oxidizer gas, a sweeping gas supply mechanism for sweeping any of the fuel and oxidizer gas flow passages by a sweeping gas, a sweeping determination mechanism for determining whether to perform sweeping by the sweeping gas supply mechanism, when receiving a stop request for stopping the fuel cell system, a pressure reduction mechanism for reducing a pressure within one of the flow passages lower than when determined not to perform the sweeping, when determined to perform the sweeping by the sweeping determination mechanism, and an actuation mechanism for actuating the sweeping gas supply mechanism after the pressure within the flow passage is reduced by the pressure reduction mechanism.