With the aim of dynamic simulation and control, a new non-linear state-space dynamic non-isothermal polymer electrolyte membrane fuel cell (PEMFC) model is developed in this paper. This mathematical model is developed based on mass and energy equation. The present model takes in account subsequent factors as the effects of charge double layer capacitance, the geometrical capacity and the effect of temperature gradient. In this paper, the authors propose a combination of several dynamic equations to study the effect of suddenly variation of some operating parameters like load resistance, gas pressure and gas temperature input. The results are compared to those of an isothermal model. This model will be extremely functional for the best possible design and real-time control of PEMFC systems. The present model is executed in MATHCAD software and the fuel cell is symbolized by an equivalent circuit which incorporates gas diffusion layer, membrane and electrodes. The analysis results show that the main elements that influence the performance of the cell are load resistance and functioning temperature. Copyright (C) 2012, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.