A fuel cell system includes a cathode gas supply passage through which cathode gas is supplied to the fuel cell stack, a cathode gas discharge passage through which the cathode gas is discharged from the fuel cell stack, a turbo compressor provided in the cathode gas supply passage for delivering the cathode gas to the fuel cell stack, a valve provided in the cathode gas supply passage or the cathode gas discharge passage, and a controller that controls constituent components of the fuel cell system including the turbo compressor and the valve. The controller performs cathode-gas flow rate change control to alternately open and close the valve, in a condition where the turbo compressor is driven, when the fuel cell stack is not required to generate electric power.