A fuel cell system, comprising: a fuel cell stack; a cathode compressor configured to supply a cathode gas; a cathode flow passage connected to the fuel cell stack, for the cathode gas to flow; at bypass flow passage branching from the cathode flow passage upstream of the fuel cell stack, thereby bypassing the fuel cell stack; a bypass valve provided on the bypass flow passage and configured to adjust a cathode flow rate flowing through the bypass flow passage; a stack flow rate sensor configured to detect a cathode flow rate supplied to the fuel cell stack; a compressor flow rate sensor configured to detect a cathode flow rate taken into the cathode compressor; a required stack flow rate calculation unit configured to calculate a flow rate required by the stack necessary for the fuel cell stack depending on a target output of the fuel cell stack; a required compressor flow rate calculation unit configured to calculate a flow rate required from the compressor depending on a requirement for surge avoidance or hydrogen off-gas dilution; and a control unit configured to control, if the flow rate required from the compressor is more than the flow rate required by the stack, the cathode compressor based on the flow rate required from the compressor and a compressor flow rate detected by the compressor flow rate sensor and control the bypass valve based on the flow rate required by the stack and a stack flow rate detected by the stack flow rate sensor, and control, if the flow rate required by the stack is more than the flow rate required from the compressor, the cathode compressor based on the flow rate required by the stack and the stack flow rate detected by the stack flow rate sensor. a fuel cell stack; a cathode compressor configured to supply a cathode gas; a cathode flow passage connected to the fuel cell stack, for the cathode gas to flow; at bypass flow passage branching from the cathode flow passage upstream of the fuel cell stack, thereby bypassing the fuel cell stack; a bypass valve provided on the bypass flow passage and configured to adjust a cathode flow rate flowing through the bypass flow passage; a stack flow rate sensor configured to detect a cathode flow rate supplied to the fuel cell stack; a compressor flow rate sensor configured to detect a cathode flow rate taken into the cathode compressor; a required stack flow rate calculation unit configured to calculate a flow rate required by the stack necessary for the fuel cell stack depending on a target output of the fuel cell stack; a required compressor flow rate calculation unit configured to calculate a flow rate required from the compressor depending on a requirement for surge avoidance or hydrogen off-gas dilution; and a control unit configured to control, if the flow rate required from the compressor is more than the flow rate required by the stack, the cathode compressor based on the flow rate required from the compressor and a compressor flow rate detected by the compressor flow rate sensor and control the bypass valve based on the flow rate required by the stack and a stack flow rate detected by the stack flow rate sensor, and control, if the flow rate required by the stack is more than the flow rate required from the compressor, the cathode compressor based on the flow rate required by the stack and the stack flow rate detected by the stack flow rate sensor.