A fuel cell system includes a fuel cell having a fuel gas flow path and an oxidant gas flow path; a compressor for supplying humidified air to the oxidant gas flow path; a back-pressure regulating valve for controlling pressure of humidified air in the oxidant gas flow path; a pressure sensor for measuring the pressure of the humidified air in the oxidant gas flow path; and a control section for controlling the compressor and the back-pressure regulating valve. In this system, the pressure of humidified air in the oxidant gas flow path is regulated to become equal or approximate to a target pressure by the back-pressure regulating valve. When the pressure difference between the pressure measured by the pressure sensor and the target pressure is larger than a predetermined pressure difference, the control section corrects operating conditions of the compressor, so that the measured pressure becomes the target pressure.