A temperature control scheme for a fuel cell stack thermal sub-system in a fuel cell system that uses a non-linear thermal model and disturbance rejection to provide an optimum stack temperature. The thermal sub-system includes a coolant loop directing a cooling fluid through the stack, a pump for pumping the cooling fluid through the coolant loop, and a radiator for cooling the cooling fluid outside of the fuel cell stack. The system includes a controller for controlling the speed of the pump so as to maintain the temperature of the stack at a desired temperature. The controller uses the thermal model to anticipate a temperature of the cooling fluid out of the fuel cell stack to control the speed of the pump.

 
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