In this work, a dynamic model of an integrated autothermal reformer (ATR) and proton exchange membrane fuel cell (PEM FC) system and model-based evaluation of its dynamic characteristics are presented. The ATR reforms JP5 fuel into a hydrogen rich flow. The hydrogen is extracted from the reformate flow by a separator membrane (SEP), then supplied to the PEM FC for power generation. A catalytic burner (CB) and a turbine are also incorporated to recuperate energy from the remaining SEP flow that would otherwise be wasted. A dynamic model of this system, based on the ideal gas law and energy balance principles, is developed and used to explore the effects of the operating setpoint selection of the SEP on the overall system efficiency. The analysis reveals that a trade-off exists between the SEP efficiency and the overall system efficiency. Finally the open loop system simulation results are presented and conclusions are drawn on the SEP operation. (C) 2007 Elsevier Ltd. All rights reserved.