At system shutdown, supply of hydrogen to a fuel electrode of a fuel cell stack is stopped, and at the same time dry air is supplied to an oxidant electrode. The dry air is subsequently supplied also to the fuel electrode, and finally the system is shut down. This allows optimal conditioning of a fuel cell at system shutdown, and effectively suppresses deterioration of a proton exchange membrane or a catalyst layer of the fuel cell which is caused at system shutdown as well as during storage. Furthermore, a fuel cell system excellent in safety and the like can be provided.