A fuel cell system including: a fuel cell supplied with a fuel gas to a fuel electrode thereof and air to an air electrode thereof; a fuel gas supplying device which supplies the fuel gas to the fuel electrode; an air supplying device which supplies air to the air electrode; a fuel gas pressure regulator which regulates fuel gas pressure at the fuel electrode; a purge valve which discharges exhaust fuel gas from the fuel electrode to the outside; and a controller. The controller continues power generation of the fuel cell, controlling the fuel gas pressure regulator to lower the fuel gas pressure at the fuel electrode, having the air supplying device continuing supplying air to the air electrode with the purge valve closed; and after the fuel gas pressure at the fuel electrode becomes equal to or lower than the atmospheric pressure, stops power generation of the fuel cell.