In a fuel cell system including a fuel cell, an anode gas supply channel, an anode gas discharge channel, an injector, a pressure sensor, and a controller, the controller controls the injector so that the pressure on the downstream side of the injector in the anode gas supply channel and does not become lower than target pressure, closes a discharge valve when the amount of discharged anode gas reaches a target discharge amount, the amount of discharged anode gas estimated based on the amount of decrease in the value of the pressure in a first period of the discharge valve open-period, the first period being a period from the point of time after the injector stops the injection and when variation of the pressure falls within a predetermined range to the point of time when the injector next starts the injection, and increases a ratio of the first period to the drive cycle by controlling, during the discharge valve open-period, at least one of the anode gas supply rate of the injector, the amount of electric power generated by the fuel cell, and the drive cycle of the injector.