A fuel cell system includes an air supply flow path configured to supply the air to a fuel cell, a reed valve provided in the air supply flow path, an air exhaust flow path configured to allow the air discharged from the fuel cell to flow therethrough, a pressure regulating valve provided in the air exhaust flow path and configured to adjust back pressure of the air supplied to the fuel cell, a bypass flow path configured to connect an upstream section of the air supply flow path upstream of the reed valve with the air exhaust flow path, and a bypass valve provided in the bypass flow path and configured to open and close the bypass flow path. The fuel cell system reduces the opening of the pressure regulating valve with supplying the air to the fuel cell in the closed position of the bypass valve, so as to increase the pressure of the air upstream of the pressure regulating valve, and subsequently opens the bypass valve.