The use of finite element simulations to characterize the operating behavior of a microchemical reactor and enhance its design is described. Important design issues for a microreactor, specifically heat and mass transfer, are explored with the design of a micro-flow sensor and the redesign of the reactor heater. The impact of the design choices for a flow sensor is quantitatively evaluated and an optimal design is proposed. This design was fabricated and testing confirmed the simulation work. The reaction channel heater was redesigned to improve thermal uniformity in the reaction zone. Simulations showed that before ignition significant non-uniformity still existed, but this was dramatically reduced after ignition. The use of previously reported kinetic models for ammonia oxidation in microreactor simulations is also discussed. It was found that kinetic models evaluated in conventional reactor experiments are inadequate for use in microreactor simulations because of the lower operating temperature and broader range of temperatures of the microreactor.