This simulation work analyzes different membrane reactor configurations applied to a 2 kW micro-cogeneration system based on Proton Exchange Membrane Fuel Cell. The adoption of membrane reactor technology achieves an overall electrical and 2nd law efficiency of about 43% and 48% respectively, in comparison to 34% and 38% with conventional fuel processor. The comparison between packed bed and fluidized bed membrane reactor shows an increase of about 25% in membrane area required for the packed bed configuration (without pre-reforming section); this difference decreases when a pre-reformer is used for the packed bed option. Furthermore, a parametric study on the effect of reactor pressure and temperature has been carried out along with an exergy analysis, showing that fuel processor and steam generator exergy losses with conventional fuel processing systems accounts for 33.6%, while membrane reformer reduces to 20.4%. Finally, the performance of a membrane reactor configuration offering the capability of CO2 capture, integrated within the fuel cell cogeneration system, is presented and discussed.