A fuel cell system includes a fuel cell; a fuel gas supplying unit supplying the fuel gas into the fuel cell on the anode side thereof; an oxidizing agent gas supplying unit supplying the oxidizing agent gas into the fuel cell on the cathode side thereof; a raw material gas supplying unit supplying the raw material gas into the fuel cell; and a controlling unit controlling the supply of the fuel gas, the oxidizing agent gas and the raw material gas. After switching the output of electric power or the fuel cell off, the fuel gas supplying unit suspends the supply of the fuel gas, the oxidizing agent gas supplying unit suspends the supply of the oxidizing agent gas and the raw material gas supplying unit supplies the raw material gas into the fuel cell to purge the fuel cell on the cathode side.