A fuel cell system supplies anode gas and cathode gas to a fuel cell and generates electric power in accordance with a load. The fuel cell system configured to include a cathode gas control unit controls a pressure of the cathode gas on the basis of the load, an anode gas control unit configured to cause a pressure of the anode gas to pulsate on the basis of the pressure of the cathode gas and a pulsation amplitude. The pulsation amplitude is determined on the basis of an operating condition of the fuel cell. The fuel cell system includes an anode gas partial pressure maintenance control unit configured to increase the pressure of the anode gas in accordance with a condition of an impurity within the fuel cell. The cathode gas control unit configured to make the pressure of the cathode gas higher when a pressure difference between the pressure of the anode gas and the pressure of the cathode gas is large than when the pressure difference is small.