To provide the fuel cell system, which can prevents the imperfect combustion of the fuel gas in combustor caused by shortage of the air exhausted from the fuel cell so that the harmful components is not contained in the exhausted gas, and can prevents the decreasing of the cell voltage by enabling drainage of the produced water from fuel cell certainly. A flow rate controller 8 is provided in the position between the air compressor 4 and the fuel cell 1 of the air supply line 6. The control unit CU is connected to the air supply line 6, and set the openings of the flow rate controller 8 as temporally wide, and a flow rate of the air supplied to the fuel cell is increased for a predetermined period of time. Then, set the opening of the flow rate controller 8 as gradually narrow, and the flow rate of the air supplied to the fuel cell is decreased gradually.