In a fuel cell system, a fuel cell includes plural stacked cells, a circulation passage for circulating a thermal medium to the fuel cell. The fuel cell has therein a plurality of thermal medium passages through which the thermal medium flows, and the thermal medium passages are provided such that the thermal medium from the circulation passage independently flows through the thermal medium passages. The thermal medium passages in the fuel cell have inlet portions from which the thermal medium is introduced, and outlet portions from which the thermal medium is discharged. In the fuel cell system, at least one-side portions among the inlet portions and the outlet portions are provided independently. Accordingly, a circulation area of the thermal medium in the fuel cell can be selectively changed, and a part of the fuel cell can be effectively heated to generate electrical power in this part.