A fuel cell system is provided with a humidifying device (27, 28) for humidifying at least one of fuel gas and oxygen-bearing gas, a water passage (11) through which water from a water tank (5) flows, a water removing device (2, 3, 3a, 4) for supplying purge gas to the water passage in order to remove the water in the water passage, and a water recirculating device (8) for enabling water to flow through the water passage. The fuel cell system is also provided with a shutoff valve (7) for blocking the water passage such that water from the water tank does not flow into the water recirculating device, the shutoff valve (7) being provided between the water tank (5) and the water recirculating device (8). When a shutdown operation of the fuel cell system begins, a controller (48) controls the shutoff valve (7) to open and controls the water removing device (2, 3, 3a, 4) such that purge gas is supplied to the water passage. The controller (48) also controls the shutoff valve (7) to block the water passage after the water has been expelled from the water passage.