A fuel cell system includes a fuel cell which generates electric power by using a hydrogen gas and an oxidizing gas, a hydrogen gas supply route where the hydrogen gas to be supplied to an anode of the fuel cell flows, an anode off-gas discharge route for discharging an anode off-gas discharged from the anode of the fuel cell to outside, an anode off-gas discharge valve provided to the anode off-gas discharge route, and a controller which causes the anode off-gas discharge valve to be opened when a temperature of any of the hydrogen gas supply route, the anode of the fuel cell, the anode off-gas discharge route, and the anode off-gas discharge valve becomes equal to or lower than a predetermined temperature.