Abstract Electronic components depend on the passage of electric current to perform their duties, and they become potential sites for excessive heating, since the current flow through a resistance is accompanied by heat generation. The heat generated must be removed by designing a suitable thermal management system for reliable operation of the electronic device. Also the size of electronic systems used in industries such as microelectronics, telecommunications, aerospace, biomedical, robotics and similar other areas are rapidly decreasing. Unless properly designed and controlled, high rates of heat generation result in high operating temperatures for electronic equipment, which jeopardizes its safety and reliability. With the advent of micro-manufacturing technology, multiple micro channels are machined on the back of the substrates of electronic components in integrated circuits. The heat generated by the electronic component is transferred to the coolant by forced convection. In the present study analysis on a rectangular microchannel heat sink was done by using water, Al2O3-water, and TiO2-water nanofluids as working fluids. The nanofluid properties were evaluated with correlations available in the literature. The hydrodynamic and thermal behavior of a microchannel was studied in the present work. The variation wall temperature, pressure drop in the channel and the heat transfer rate was calculated. The effect of Reynolds number on heat transfer in the microchannel was also studied. A significant improvement in the heat transfer was found with microchannel heat sink due to decrease in convective heat transfer resistance as the size of the thermal boundary layer decreased with microscopic size of the channels. It was also found from the simulation results that there was no extra pressure drop at low volume fractions of nanoparticles in the base fluid. The simulation results generated were compared with the analytical data available in the literature and found good agreement.