The theme of the present invention is a fuel cell system capable of avoiding a disadvantage caused by the maintaining of a low-efficiency operation to improve the safety of a system operation. The fuel cell system is configured to perform the low-efficiency operation having a large power loss as compared with a usual operation at a predetermined low temperature to raise the temperature of a fuel cell in a short time as compared with the usual operation. The fuel cell system prohibits the low-efficiency operation to execute the usual operation, in a case where predetermined conditions are established at the predetermined low temperature. The predetermined conditions include a time when the generated power of the fuel cell cannot be consumed, a time when this generated power cannot be accumulated in a battery, or a time when the flooding of the fuel cell is generated.