A fuel cell system includes a compressor provided in a cathode gas supply passage configured to feed the cathode gas under pressure to the fuel cell, a bypass passage configured to discharge the cathode gas fed under pressure by the compressor to a cathode gas discharge passage while bypassing the fuel cell, a bypass valve provided in the bypass passage and configured to adjust a flow rate of the cathode gas flowing in the bypass passage, a system stopping unit configured to stop the fuel cell system by performing a predetermined stop sequence process when a request to stop the fuel cell system is made, and a stop-time bypass valve control unit configured to control a valve body of the bypass valve to a predetermined initialization position in parallel with the sequence process during the stop sequence process.