A method of driving a fuel cell system according to embodiments of the present invention includes supplying a first amount of oxidizer (which is less than a normal amount of oxidizer) to a fuel cell stack while continuously supplying fuel to the fuel cell stack, supplying a second amount of oxidizer (which is more than the normal amount) to the fuel cell stack, and supplying a third amount of oxidizer (which is the normal amount of oxidizer supplied in a normal driving state) to the fuel cell stack.