A fuel cell system includes a fuel cell having an anode, a cathode, and an electrolyte membrane disposed therebetween. An oxidant gas supplying device supplies oxidant gas to the cathode, an oxidant gas backpressure regulating device regulates the pressure of the oxidant gas at the cathode according to a valve opening, and a pressure detecting device detects the oxidant gas pressure at the cathode. During a start-up fuel gas disposal process, a controller controls the oxidant gas supplying device to supply the oxidant gas at a standard oxidant gas flow, controls the valve opening of the oxidant gas backpressure regulating device to a first valve opening, and controls the valve opening of the oxidant gas backpressure regulating device to a second valve opening which is greater than the first valve opening when the oxidant gas pressure detected by the pressure detecting device reaches an elevation target pressure.