A fuel cell system increases an output voltage of a fuel cell if an electric power generation command value Pref for the fuel cell abruptly reduces while the fuel cell is being warmed up at a low-efficiency operation, which has lower electric power generation efficiency than that of a normal operation. Thus, the surplus electric power Ws corresponding to the difference between an electric power generation amount Pmes of the fuel cell and the electric power generation command value Pref is stored into a capacitive component of the fuel cell, thereby matching the electric power supplied to an external load of the fuel cell (Pmes-Ws) with the electric power generation command value Pref. This makes it possible to conduct control not to supply the surplus electric power to the external load when the electric power required from the fuel cell suddenly reduces during the low-efficiency operation.