There is provided a fuel cell system that generates an electric power by supplying an anode gas and a cathode gas to a fuel cell. The fuel cell system includes: auxiliary machines and a drive motor driven by the generated electric power of the fuel cell; a pressure control unit configured to control a pressure of the cathode gas to be supplied to the fuel cell at a normal target pressure, the normal target pressure being used for ensuring an oxygen partial pressure within the fuel cell in accordance with the generated electric power of the fuel cell; and a warming-up pressure control unit configured to control the pressure of the cathode gas to be supplied to the fuel cell to become a predetermined warm-up acceleration target pressure during warm-up of the fuel cell, the predetermined warm-up acceleration target pressure being higher than the normal target pressure. In a case where there is a request to drive the drive motor during the warm-up of the fuel cell, the warming-up pressure control unit controls the pressure of the cathode gas to be supplied to the fuel cell to a warm-up target pressure between the normal target pressure and the warm-up acceleration target pressure.