According to an embodiment disclosed herein, a fuel cell system includes a cooling line through which cooling water passing through a plurality of electronic parts circulates and in which a wire for supplying power to the plurality of electronic parts is disposed, a pump that is connected to the cooling line and pumps the cooling water, a cooling fan that cools the cooling water, and a controller that determines a control mode based on a temperature of the wire and controls the number of rotations of the pump and the number of rotations of the cooling fan based on the control mode.