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The aim of the present numerical investigation is to analyze the effects of transverse magnetic field on heat transfer and fluid flow characteristics in a rectangular microchannel heat sink (MCHS). The effects of Hartmann number, channel aspect ratio, total channel height and total channel width on heat transfer and fluid flow characteristics are widely investigated. The governing equations for three-dimensional steady, laminar flow and conjugate heat transfer of a microchannel are solved using the finite volume method. The obtained results are discussed with various combinations of pertinent parameters involved in the study. The results reveal that magnetic field can enhance the thermal performance of the MCHS but it is accompanied with a slight increase in pressure drop.