A fuel cell system includes a first converter to convert power, which is output from a fuel cell stack or a battery, into power in a specific level, a second converter to convert power which is input to or output from the battery, a power relay assembly to control power flow between a super capacitor and the first converter, and a controller to control outputs of the first converter and the second converter, depending on a starting state or an operating state of the fuel cell system, and to control an operation of the power relay assembly.