The present invention has been devised in order to solve the problems described above, and an object of the present invention is to provide a fuel cell system that can discharge an impurity in an anode gas flow channel while suppressing wasteful discharge of a fuel gas to the outside of the system. An exhaust valve is connected to a downstream end of an anode gas flow channel of a fuel cell. The exhaust valve has an exhaust mode in which a substantially smaller amount of gas than the consumption of a fuel gas in the anode gas flow channel is discharged to the outside of the system. After a request to stop electric power generation by the fuel cell, the output current value of the fuel cell is increased to a predetermined value. Then, the exhaust valve is set in the exhaust mode before or when the output current value is increased, and the discharge flow rate of the exhaust valve is increased in accordance with the increase of the output current value.