A coolant temperature control system for a fuel cell stack in a vehicle includes a controller for determining a real time target exit temperature of a fuel cell stack coolant and a communicating device for detecting a fuel cell voltage and a fuel cell current outputted from the fuel cell stack. The real time target exit temperature of the fuel cell stack coolant is determined by an input fuel cell heat to fuel cell power ratio generated from the fuel cell stack for compensating the target exit temperature due to degradation of the fuel cell stack over time. In addition, the coolant temperature control system determines to activate for evaluating the real time target exit temperature of the fuel cell stack coolant when a trip distance of the vehicle is greater than a predetermined travel distance.