Abstract Methanol reforming offers an attractive source of hydrogen for proton exchange membrane fuel cell (PEMFC) systems for portable power. At present, the greatest obstacle to realization of these systems is the extraction of hydrogen from the hydrocarbon fuel, i.e., the fuel processing part. Because of size and portability, microchemical technology has shown assuring results in the field of fuel processing. However, several roadblocks persist in the development of an integrated micro-fuel processor and fuel cell system. Thermal management in miniature systems is perhaps the most crucial of these challenges. In this study, a silicon microreactor-based catalytic methanol steam reforming reactor was demonstrated in the context of complete thermal integration to understand this critical issue. Detailed experiments were carried out to quantify heat losses through various pathways from the planar microreactor structure. Based on these experiments, an empirical correlation is developed to predict natural convection heat transfer coefficient from meso to microscale devices. The result provides fundamental insight of critical thermal issues such as transfer of heat between reactor components, control of temperature, insulation, and heat losses. Based on this understanding, suggestions are made for scale up of reactor components and a packaging scheme for reduction of convective and radiative losses.