In a fuel cell system, during the state where the fuel cell system is not generating an electric power, a fuel gas passage and an oxidizing gas passage are closed, and an inert gas supply device (54, 58) supplies an inert gas to an anode space (111) which is substantially isolated from outside, the anode space including the closed fuel gas passage and a space connected to the closed fuel gas passage, while an air supply device (67, 70) supplies air to a cathode space (112) which is substantially isolated from outside, the cathode space including the closed oxidizing gas passage and a space connected to the closed oxidizing gas passage. With this, the fuel cell system is capable of achieving high energy efficiency and of surely preventing degradation of electrodes during the state where the fuel cell system is not generating the electric power, irrespective of repeated start-up and stop.