The present invention provides a fuel cell system having means for controlling the flow of coolant within a fuel cell system. A desirable rate of flow of coolant is created, during power generation, by determining the difference in temperature between coolant flowing into individual cell sets of the fuel cell assembly and the temperature of coolant exhausted from the cell assembly. The fuel cell system features controls adapted to evaluate the heat generation state of each fuel cell set and to regulate the temperature of cell sets by controlling the rate circulation of the coolant.