A fuel cell system includes a fuel cell stack, a compressor that supplies cathode gas to the fuel cell stack, and a controller that controls constituent components of the fuel cell system including the compressor. The controller controls the compressor, such that a supply period in which the compressor supplies the cathode gas and a stop period in which supply of the cathode gas is stopped appear alternately, when the fuel cell stack is not required to generate electric power, and the supply period is longer than the stop period, and such that the flow rate of the cathode gas supplied by the compressor in the supply period is smaller than the flow rate in the case where the fuel cell stack is required to generate electric power.