A fuel cell system includes a compressor for supplying the cathode gas to the fuel cell, an anode gas discharge system for discharging anode off-gas discharged from the fuel cell into a cathode gas flow passage, a pulsating operation control unit for causing a pressure of the anode gas to pulsate based on an operating state of the fuel cell, a purge control unit for purging the anode off-gas into the cathode gas flow passage based on an impurity concentration of an anode of the fuel cell and a pressure of the anode, and a compressor control unit for controlling the compressor based on a purge flow rate controlled by the purge control unit, and the purge control unit for setting the pressure of the anode to a predetermined value determined according to a pulsating state of the anode gas.