A fuel cell system includes fuel cell units each including a fuel cell stack, an anode gas discharge system configured to discharge anode gas from the fuel cell stack, and a cathode gas supply and discharge system configured to supply cathode gas to the fuel cell stack and discharge cathode gas from the fuel cell stack, a mixed gas discharge system configured to mix gas discharged from the anode gas discharge system and the cathode gas supply and discharge system of each fuel cell unit and discharge the mixed gas, and a controller configured to control the fuel cell units. The controller is configured to control at least one of the anode gas discharge system and the cathode gas supply and discharge system of each fuel cell unit to shift a time at which gas to be discharged from each fuel cell unit merges in the mixed gas discharge system.