A fuel cell system which is capable of reducing deterioration of fuel cells includes a cell stack, a CPU, a voltage detection circuit, a current detection circuit, an external air temperature sensor, a humidity sensor, a concentration sensor and sonars. The CPU obtains a volume of a garage, an amount of temperature change, an amount of humidity change and an amount of methanol concentration change in external air, as well as an amount of output change in the cell stack based on detection results from the voltage detection circuit, the current detection circuit, the external air temperature sensor, the humidity sensor, the concentration sensor and the sonars. The CPU sets first through fifth duration times based on the volume of the garage and the various amounts of changes, selects the shortest duration time, and stops power generation in the cell stack when the selected duration time has passed.