Owing to the pollution free nature, higher efficiency and noise free operation, fuel cells have been identified as ideal energy sources for the future. To avoid direct storage of hydrogen due to safety considerations, storing hydrocarbon fuel such as methane and suitably reforming in situ for hydrogen production offers merit for further investigation. Separating the resulting hydrogen in the reformate using membrane separation can directly feed pure gas to the anode side of fuel cell for power generation. Despite the numerous works reported in literature on the dynamic and steady state modeling and analysis of reformers, membrane separation units and fuel cell systems, there has been limited work on an analysis of the integrated system consisting of all the three components. This study focuses on the mathematical modeling and analysis of the integrated reformer, membrane, fuel cell system from first principles in a dynamic framework. A multi loop control strategy is developed and implemented on the mathematical model of the integrated system in which appropriate controllers based on the system dynamics are designed to examine and study the overall closed loop performance to achieve rapidly fluctuating target power demand and rejection of reformer feed and fuel cell coolant temperature disturbances.