Joule heating effects on a slit microchannel filled with electrolytes are comprehensively investigated with emphasis on the thermal boundary conditions. An accurate analytical expression is proposed for the electrical field and the temperature distributions due to Joule heating are numerically obtained from the energy balance equation. The results show that a thermal design based on the average electric potential difference between electrodes can cause severe underestimation of Joule heating. In addition, the parame- tric study of thermal boundary conditions gives us an insight into the best cooling scenario for microfluidic devices. Other significant thermal characteristics, including Nusselt number, thermophoretic force, and entropy generation, are discussed as well. This study will provide useful information for the optimization of a bioMEMS device in relation to the thermal aspect.