A system and method for determining the internal temperature of a fuel cell stack during stack start-up so as to start a cooling fluid flow before the internal temperature of the stack rises above a temperature that might damage the fuel cells within the stack. The system and method include determining an initial temperature from either an ambient temperature sensor or a sensor in the cooling fluid manifold in the stack, measuring the voltage of the stack and the current from the stack, and from these values determining the waste heat from the stack to determine its temperature. If hydrogen is sent to the cathode side of the stack during the start-up, then the system and method also include determining the flow rate of the hydrogen.