A fuel cell system employs a fuel cell stack having an air electrode, an electrolyte membrane, and a fuel electrode. The fuel cell system includes an air residual space, from which air supplied to the air electrode is not discharged to stay behind therein when the fuel cell system is stopped. The air residual space communicates with the air electrode. The fuel cell system includes a hydrogen residual space, from which hydrogen supplied to the fuel electrode is not discharged to stay behind therein when the fuel cell system is stopped. The hydrogen residual space communicates with the fuel electrode. A residual ratio satisfies a specific reference range and corresponds to a ratio of the molecular number of hydrogen that stays behind in the hydrogen residual space to the molecular number of oxygen in air that stays behind in the air residual space when the fuel cell system is stopped.