In a fuel cell system, a controller is programmed to control a first gas supply mechanism to deliver a first gas containing a fuel gas to a cathode in a pre-stop process performed at a system stop of the fuel cell system. The controller is programmed to control the first gas supply mechanism to stop the delivery of the first gas in a first state where a partial pressure difference between an anode and the cathode with respect to at least the fuel gas of remaining gases in the anode and in the cathode is reduced to or below a preset reference value.