Flow rate nonuniformities (termed as maldistribution) among a stack of microchannels connected with each other through the inlet/outlet plenums of a microchannel heat sink (MCHS) are one of the major hindrances associated with effective and efficient operations. That induces many undesirable effects, including accentuation of lateral and flow direction nonuniformities in surface temperatures (for uniform heat flux loads). This can lead to feedback-induced lateral heat flow in the electronics underneath the MCHS, which is to be avoided. For the reported numerical study of single-phase liquid cooling, a new flow maldistribution mitigation technique—involving splitting of the single inlet port to the inlet manifold (conventional) into two separate inlet ports—is proposed, and the results are compared with the conventional method. The proposed scheme helps in reducing the flow maldistribution (its measure defined in this paper) problem. In the case of two ports, in the front of the inlet manifold, the reduction is about 26.2%, and in the case of one suitably placed port on each side of the inlet manifold, the flow rate maldistribution is reduced by about 68.5%, and in addition, the MCHS efficiency (defined as heat-carrying capacity per unit pumping power) is improved by 7.7%.