A fuel cell system calculates a target value of a flow rate of cathode gas to be supplied to a fuel cell stack according to a request of the fuel cell stack, controls a flow rate of the cathode gas to be supplied by the compressor according to an operating state of the fuel cell system, controls a bypass valve based on a target fuel cell supply flow rate so that the flow rate of the cathode gas to be supplied from the compressor to the fuel cell stack reaches the target fuel cell supply flow rate, and limits the flow rate of the cathode gas to be supplied by the compressor when the bypass valve has a predetermined opening and the flow rate of the cathode gas to be supplied to the fuel cell stack is not smaller than the target fuel cell supply flow rate.