A fuel cell system includes a fuel cell stack, a compressor, a cathode flow passage, a bypass flow passage branching from the cathode flow passage, thereby bypassing the stack, a bypass valve adjusting a bypass flow rate, a stack flow rate sensor detecting a flow rate to the stack, and a compressor flow rate sensor detecting a flow rate into the compressor. A flow rate for the stack depending on a state of a fuel cell and a flow rate the compressor controls depending on a requirement different from that of the stack are calculated. A control unit controls, when the flow rate required from the compressor is more than that required by the stack, the compressor based on the flow rate required from the compressor and a detected compressor flow rate, and controls the bypass valve based on the flow rate required by the stack and a detected stack flow rate.