Fuel cell based modular power generation can be achieved by miniaturization and process intensification of equipments in the process. Fuel cells require hydrogen rich gas which can be generated through reforming and water gas shift reaction. The water gas shift reactor being kinetically limited occupies more volume to achieve the required CO conversion. A membrane reactor integrates the reaction and hydrogen separation stages and hence reduces the volume requirement. Computational Fluid Dynamics offers virtual prototyping of the reactor and thus helps in design, optimization and scale up of reactors. In this study customized User Defined Functions (UDFs) were developed to analyze the performance of low temperature water gas shift membrane reactor. The models were validated using literature data for the parameters - synthesis gas compositions, time factor, sweep flow rate and steam to CO ratio. The effect of all these parameters on the reactor was analyzed for CO conversion, H2 recovery, DaPe, concentration polarization, concentration profiles and conversion index. The simulations have showed that the UDFs developed were capable of simulating the membrane reactor and this can be used for the design and optimization of the membrane reactor for any process conditions. © 2011 The Institution of Chemical Engineers.