A fuel cell system includes a fuel cell stack that includes a plurality of unit cells, each including a membrane-electrode assembly including an electrolyte membrane, a cathode at one side of the electrolyte membrane, and an anode at an opposite side of the electrolyte membrane, and separators at respective sides of the membrane-electrode assembly, a fuel supply for supplying a fuel to the fuel cell stack, an oxidizing agent supply for supplying an oxidizing agent to the fuel cell stack, and a controller for controlling operation of the fuel supply and the oxidizing agent supply, for measuring a voltage of each of the unit cells, and for turning off a load coupled to the fuel cell stack after determining that the voltages of the unit cells reached a reference voltage.