A fuel cell system and a method of operating the same, the fuel cell system comprising: a fuel cell including at least one unit cell; an switch having first and second ends connected to different type electrodes of the fuel cell; and a circuit unit to detect whether a load is applied to the fuel cell, to control the operation of the switch according to the detection, cycle the switch open and closed to short circuit the fuel cell, in order to prevent the fuel cell from overheating and to consume a residual fuel in the fuel cell. The fuel cell system may further include a converter, a secondary cell, a battery charger, and a switching unit between the load and the fuel cell.