A fuel cell system includes a fuel cell, a cathode supply passage, a cathode discharging passage, an anode supply passage, an anode discharging passage, a pair of cathode shutoff units, an anode shutoff unit, an anode discharging unit, a discharged gas processing unit, and a control unit. The control unit releases the sealing of the cathode passage by the pair of cathode shutoff units, at the time of start-up of the fuel cell system, and releases the sealing of the anode passage by the anode discharging unit, thereby performing a purge process to allow discharge of the anode gas.