A fuel cell system and a method of controlling the same are provided. The fuel cell system includes a supplying pipe that supplies hydrogen and air to a stack and a gas concentration sensor that senses hydrogen and air impurities supplied to the supplying pipe. A supplying valve is disposed in the supplying pipe to adjust the hydrogen and air supply and a discharging pipe discharges the hydrogen and the air from the stack. A discharging valve is disposed in the discharging pipe to adjust the discharging of the hydrogen and the air. A controller operates with the gas concentration sensor to detect introduction of the impurities. Exhaust valves are disposed at the front and rear end of the stack to remove a polluted fuel when the impurities are introduced. When performance deteriorates due to the impurities, a cause of deterioration is determined, and stack performance is recovered.