A fuel cell system, comprising: a fuel cell stack; a first cooling medium circuit through which a cooling medium for cooling the fuel cell stack flows; an ion exchanger provided in the first cooling medium circuit and configured to remove ions in the cooling medium flowing in the first cooling medium circuit; a second cooling medium circuit which is allowed to be connected to the first cooling medium circuit and in which average ion concentration of the cooling medium is lower than that of the cooling medium in the first cooling medium circuit, the average ion concentration being average ion concentration of the cooling medium while flow of the cooling medium is stopped; a switching valve configured to switch between a flow state and a low flow state, the flow state being a state in which the cooling medium having flowed through the second cooling medium circuit flows into the first cooling medium circuit, and the low flow state being a state in which the flow of the cooling medium from the second cooling medium circuit into the first cooling medium circuit is reduced as compared to the flow state; a pump configured to cause the cooling medium in the second cooling medium circuit to flow into the first cooling medium circuit when the switching valve is in the flow state; and a control unit configured such that, when a stop period, which is a period from a time the fuel cell system is stopped until an instruction to start the fuel cell system is input, is longer than a predetermined reference period, the control unit drives the pump with the switching valve switched to the flow state after the instruction to start the fuel cell system is input. a fuel cell stack; a first cooling medium circuit through which a cooling medium for cooling the fuel cell stack flows; an ion exchanger provided in the first cooling medium circuit and configured to remove ions in the cooling medium flowing in the first cooling medium circuit; a second cooling medium circuit which is allowed to be connected to the first cooling medium circuit and in which average ion concentration of the cooling medium is lower than that of the cooling medium in the first cooling medium circuit, the average ion concentration being average ion concentration of the cooling medium while flow of the cooling medium is stopped; a switching valve configured to switch between a flow state and a low flow state, the flow state being a state in which the cooling medium having flowed through the second cooling medium circuit flows into the first cooling medium circuit, and the low flow state being a state in which the flow of the cooling medium from the second cooling medium circuit into the first cooling medium circuit is reduced as compared to the flow state; a pump configured to cause the cooling medium in the second cooling medium circuit to flow into the first cooling medium circuit when the switching valve is in the flow state; and a control unit configured such that, when a stop period, which is a period from a time the fuel cell system is stopped until an instruction to start the fuel cell system is input, is longer than a predetermined reference period, the control unit drives the pump with the switching valve switched to the flow state after the instruction to start the fuel cell system is input.