A polymer electrolyte fuel cell (PEFC) is an electrochemical device that converts chemical energy directly to electrical energy, and its performance greatly depends on its operating temperature. Therefore, in this paper, a novel thermodynamic PEFC model with the airflow cooling method is firstly developed for the PEFC system. Then, a novel model predictive control (MPC) controller is designed to control the stack temperature at an optimal value by adjusting the air flow rate on the basis of the developed thermodynamic PEFC model. The thermodynamic PEFC model and the designed controlling strategies are simulated and analysed in Matlab/Simulink. Three tests are conducted to estimate the reliability of the developed controllers concerning different operating conditions: (a) typical perturbation in the current load, (b) any perturbation in the current load, and (c) variation of the ambient temperature. The simulation results demonstrate that the MPC controller can effectively control the stack temperature at the desired value. Moreover, the MPC controller shows much superior effects compared with the conventional proportional integral derivative (PID) controller. In addition, the developed coolant circuit model can be easily applied to various PEFC systems. The MPC controller shows potential also for other controlling issues of PEFC systems due to its strong robustness and fast response.