A fuel cell system comprises a fuel cell, which generates power by supplying anode gas and cathode gas into the fuel cell, a compressor, which controls the amount of the gas to be supplied into the fuel cell, and a pressure control valve, which controls the gas pressure of the fuel cell. The pressure control valve is provided on the downstream of the fuel cell. The fuel cell is controlled by changing an amount of the supply gas by the compressor, and thereafter changing the opening of the pressure control valve during the transition period of the fuel cell.