A fuel cell system includes: a first fuel cell stack and a second fuel cell stack; a supply passage connected to an inlet of oxidant gas in the first fuel cell stack; an discharge passage connected to an outlet of the oxidant gas in the second fuel cell stack; introduction unit that introduces water in the oxidant gas flowing through the discharge passage into the supply passage; and a controller configured to perform refresh control of the first fuel cell stack by lowering voltage of the first fuel cell stack, and operates, during the refresh control, the introduction unit while keeping the second fuel cell stack in an electric power generation state.