A fuel cell system includes: a fuel cell; an anode gas supply flow path for supplying an anode gas to the fuel cell; an anode gas discharge flow path for discharging an anode off gas from the fuel cell; an anode gas circulation flow path for connecting the anode gas supply flow path and the anode gas discharge flow path to each other; a circulation device provided on the anode gas circulation flow path and serving for supplying the anode off gas to the anode gas supply flow path; and a controller. When liquid water is residing in the circulation device, the controller controls a circulation flow rate of the circulation device to discharge the liquid water residing in the circulation device. The controller restricts an increasing rate of the circulation flow rate of the circulation device if it is decided that a quantity of the liquid water residing in the circulation device is equal to or more than a specified value.