A fuel cell system of the present invention includes: a fuel cell (1) having an electrolyte membrane (2), an anode (3) and a cathode (4) sandwiching the electrolyte membrane (2), a cathode gas passage (98) through which an oxidizing gas is supplied to and discharged from the cathode (4), and an anode gas passage (97) through which a fuel gas is supplied to and discharged from the anode (3); a fuel gas channel having an anode gas passage (97) and through which the fuel gas is supplied to and discharged from the anode (3); and an oxidizing gas channel having the cathode gas passage (98) and through which the oxidizing gas is supplied to and discharged from the cathode (4). When the fuel cell system stops generating electric power, the fuel gas channel and the oxidizing gas channel are closed, and a gas is supplied from a downstream side of the cathode gas passage (98) to an oxidizing gas filled space (112) which is practically isolated from outside by closing the oxidizing gas channel and includes the cathode gas passage (98).