A fuel cell system with a muffler to reduce noise generated while supplying air to a fuel cells disclosed. One embodiment of the fuel cell system includes an air feeder to supply air; an electric generator to generate electricity through an electrochemical reaction between air and fuel; and a muffler provided in one end of the air feeder. The muffler includes a first pipe and a second pipe which are different in length from each other. The muffler has a relatively small structure, so that limitation in a mounting space can be decreased and a more compact fuel cell system can be realized. Also, even if there are considerable noise components at two or more frequencies, the mufflers corresponding to the respective frequencies are connected in series, thereby reducing the noise.