In this paper, a mathematical model focuses on studying the thermal management and its effect on cell performance using a set of equations including electrochemical kinetics and thermodynamics governing the operation of a protonic ceramic fuel cell (PCFC). The model presents an approach to predict the behavior of the mass transport of gases through the PCFC and the impact of optimizing the reactants flow rates will be useful for the water and exhaust gases management program for the cell. Additionally, the fuel cell energy balance is formulated in order to properly design a balanced system of PCFC. Moreover, the pressure drop across the flow channels is discussed as a crucial parameter affecting the fuel cell performance. The supplied air excess ratio and operating temperature impactson the PCFC performance are investigated. The overall performance of PCFC systems is significantly influenced by ohmic, concentration, and activation polarizations. The modeling simulation results agreed satisfactorily with the experimental results from literature.