A fuel cell system includes: a fuel cell stack including a plurality of cells, each of which has a fuel electrode, an air electrode, and an electrolyte, and performs a power generation by a reaction between a fuel gas and air; a fuel supplier supplying the fuel gas to the fuel electrode; an air supplier supplying the air to the air electrode; a voltage detector detecting the voltage of the fuel cell stack; and a controller stopping the supplying of the fuel gas by the fuel supplier and the supplying of the air by the air supplier when the voltage of the fuel cell stack detected by the voltage detector is decreased to be lower than a threshold voltage after the power generation of the fuel cell stack is stopped.