A fuel cell system includes a gas supply passage configured to supply one of the anode gas and the cathode gas to the fuel cell, a refrigerant supply apparatus that supplies refrigerant for cooling the fuel cell to the fuel cell, a heat exchanger that exchanges heat between the refrigerant increased in temperature by the fuel cell and the gas supplied to the gas supply passage. The fuel cell includes a component that circulates the one of the anode gas and the cathode gas discharged from the fuel cell to the fuel cell, and a warm-up control unit that controls a flow rate of the refrigerant to a predetermined flow rate for warming up the fuel cell when the fuel cell is warmed up. The fuel cell system includes a gas temperature increase control unit increases the flow rate of the refrigerant to be supplied to the heat exchanger on the basis of a temperature of the gas circulated by the component or a parameter related to the temperature when the flow rate of the refrigerant is controlled by the warm-up control unit.