A study of the heat and mass transfer, flow, and thermodynamics of the reacting flow in a catalytic microreactor is presented. Methanol reforming is utilized in the fuel processing system driving a micro-scale proton exchange membrane fuel cell. Understanding the flow and thermal transport phenomena as well as the reaction mechanisms is essential for improving the efficiency of the reforming process as well as the quality of the processed fuel. Numerical studies have been carried out to characterize the transport in a silicon microfabricated reactor system. On the basis of these results, optimized conditions for fuel processing are determined.