A fuel cell system includes a fuel cell, a control valve and a controller. The controller controls the control valve to periodically increase and decrease the anode gas pressure downstream of the control valve. The controller executes a shutdown operation of the fuel cell by closing the control valve to stop the anode gas and shutting down power generation of the fuel cell upon receiving a shutdown command. The controller estimates an anode gas concentration at a location where the anode gas concentration is locally lower within a power generation region of the fuel cell based on a control state of the anode gas at a time the shutdown command is issued. The controller determines whether to permit or prohibit shutting down the power generating operation based on the anode gas concentration.
