A fuel cell system includes a fuel cell stack for power generation by electrochemical reactions of a fuel gas and an oxygen-containing gas, a high voltage energy storage capable of storing and discharging electrical energy generated by power generation of the fuel cell stack, and capable of being directly coupled to the fuel cell stack, a group of loads consuming at least electrical energy generated by the fuel cell stack or electrical energy discharged from the high voltage energy storage, and an auxiliary device control unit for reducing an amount of electrical energy remaining in the energy storage to a predetermined value by any of the group of loads, before starting power generation of the fuel cell stack.