A fuel cell system whose fuel loss caused by the crossover of the fuel is small and which can be operated economically. The fuel cell system includes a fuel cell 10, a primary feeding system 12 for feeding a primary fuel which is a liquid fuel to the fuel cell 10, a secondary feeding system 13 for feeding a secondary fuel which is a liquid fuel whose saturation vapor pressure is lower than that of the primary fuel to the fuel cell 10, a ECU 30 for controlling each part so that the primary fuel in the fuel cell is replaced with the secondary fuel when terminating the operation of the fuel cell 10.