A fuel cell system includes: a fuel cell; a compressor; a turbine; an electric motor; a first transmission configured to change a gear ratio between the compressor and the electric motor, the first transmission being linked to the compressor rotating shaft and the motor rotating shaft; and a second transmission configured to change a gear ratio between the turbine and the electric motor, the second transmission being linked to the turbine rotating shaft and the motor rotating shaft. A gear ratio of the first transmission and a gear ratio of the second transmission are set such that a rotating speed of the electric motor is lower than a rotating speed of the compressor and a rotating speed of the turbine and such that a rotating speed of the compressor is higher than the rotating speed of the turbine.