Joule heating effects on a rectangular orifice in microchannel filled with electrolyte containing nanobubbles are comprehensively investigated with emphasis on the thermal boundary conditions. Numerical studies are performed for the velocity and temperature fields to show the various aspects of fluid flow and thermal design in rectangular shaped microchannels. Furthermore the correlations for the maximum temperature increase were presented for several geometry parameters and thermal boundary conditions which gives us an insight to the best cooling scenario of microfluidic rectangular orifices. This study will provide useful information for the optimization of a bioMEMS device in thermal aspect and benefits of nano-bubble injection for temperature control. It is shown that the cooling from the side is superior in reducing the peak temperature of the micro-orifice. (C) 2015 The Institution of Chemical Engineers. Published by Elsevier B.V. All rights reserved.