A fuel cell system of the present invention is provided with a fuel cell, a fuel gas supply system that supplies a fuel gas to the fuel cell, and an oxidant gas supply system that supplies an oxidant gas to the fuel cell, and, when operation end processing is started, a flow rate of the fuel gas supplied to the fuel cell is increased only by a predetermined amount that is determined based on a temperature environment of the fuel cell system. As a result, when the operation of the fuel cell system is ended, the fuel gas at the optimum flow rate in accordance with the temperature environment is provided, thereby efficiently preventing deterioration of the fuel cell after the end of the operation.