In a fuel cell system, a controller is configured to, to stop the fuel cell system, (a) execute an oxidizing gas consumption process by supplying a fuel gas to an anode and sweeping current from a fuel cell while a supply-side on-off valve and an exhaust-side on-off valve are closed to seal the remaining oxidizing gas in the cathode, and (b) stop sweeping the current at a time point at which the difference between pressure of the cathode that decreases in response to the sweeping of the current and an estimated pressure value of the cathode that decreases by consumption of the oxidizing gas remaining in the cathode in response to the sweeping of the current becomes larger than a predetermined determination threshold value to end the oxidizing gas consumption process.