A fuel cell system is provided. The system includes a fuel cell stack, a plurality of valves operated to be selectively opened or closed to supply fuel to the fuel cell stack and remove impurities, and a pressure sensor that detects a state of pressure of fuel supplied to the fuel cell stack. A fuel cell controller then determines whether the pressure sensor or the plurality of valves are faulty by comparing increase or decrease time of the pressure detected by the pressure sensor with a reference range of time delay, as the plurality of valves are operated to be opened or closed.