A fuel cell system includes an accumulated current value measuring unit. The accumulated current value measuring unit measures an accumulated current value by time integration of current output from the fuel cell in a period during which oxygen is produced by water-splitting reaction in an anode of a negative voltage cell. A control unit uses a first correlation between the accumulated current value in the oxygen generation period and an oxygen consumption rate in the anode and a second correlation between a current density of the fuel cell in the oxygen generation period and an oxygen production rate in the anode to obtain a current density at or below which the amount of oxygen in the anode may be reduced, and causes the fuel cell to output electric power at a current density lower than the obtained current density.