The pressure-adjusting valve provided in the cathode outlet of a fuel cell stack constituting a fuel cell system has a function of adjusting the oxidizing gas pressure in the fuel cell stack according to the adjustment of the valve opening degree. When the exhaust pipe is flooded with water, the pressure inside the exhaust pipe varies from the atmospheric pressure and the opening degree of the pressure-adjusting valve changes. The flooding estimation signal output processing unit of the control unit outputs a flooding estimation signal indicating that the exhaust pipe is flooded when an opening degree difference that is a difference between the opening degree of the pressure-adjusting valve and a preset opening degree corresponding to the operation directed pressure is equal to or greater than a preset threshold opening degree difference. The processing of inhibiting the flowing is performed based on this signal.