A fuel cell system has a fuel cell, a fuel supply device, a gas discharge valve, a voltage detecting device and a control device. The fuel supply device supplies a fuel gas to the fuel cell. The gas discharge valve discharges the fuel gas into an external environment. The voltage detecting device detects an output voltage of the fuel cell. The control device controls a discharging process when a request for starting the fuel cell is given. The discharging process includes introducing the fuel gas from the fuel supply device into a predetermined passage, opening the gas discharge valve and discharging residuals staying in the passage into the external environment. When the control device receives the request and determines that the output voltage has reached a first threshold before the discharging process has not been completed, the control device starts power generation irrespective of completion of the discharging process.