A fuel cell system is provided including heating means for heating up heat medium that exchanges heat with a fuel cell, and in which the fuel cell is warmed up by the heat medium heated by the heating means. The system includes: flow rate detecting means for detecting a flow rate of the heat medium flowing through the heating means; and heat controlling means for controlling the heating means based on the flow rate of the heat medium detected by the flow rate detecting means. With this arrangement, it is possible to prevent overheating of the heat medium in the fuel cell system in which the heat medium is heated to warm up the fuel cell.