A fuel cell system includes: a fuel cell stack which receives a fuel gas and an oxidation gas to generate a power; an air compressor which supplies the oxidation gas to the fuel cell stack; and a controller which reduces the oxidation gas flow rate supplied from the air compressor to the fuel cell stack in consideration of discharge from a capacitance component of the fuel cell stack when decreasing the output voltage of the fuel cell stack. When the output voltage of the fuel cell stack has dropped, the fuel cell system can control a cell operation in consideration of the discharge from the capacitance component of the fuel cell stack to an external load.