Thermal performance of microchannel heat sink can be augmented by designing inlet/outlet manifolds such that fluid flow distribution is uniform across microchannels. In this work, the effect of inlet/outlet manifold configurations on the thermo-hydrodynamic performance of recharging microchannel heat sink (RMCHS) is investigated numerically. For this purpose branched, rectangular, trapezoidal, and triangular manifold configurations are considered. All the numerical simulations are performed for channel Reynolds number of 50–300 and constant heat flux of 10 W/cm2 applied on the substrate bottom surface of the RMCHS. The results reveal that branched manifold configuration shows uniform fluid flow distribution across all the microchannels of heat sink and also shows uniform temperature distribution on the substrate bottom surface of RMCHS. Branched manifold configuration reduces thermal resistance by 16% and enhances average Nusselt number by 9.5% compared to rectangular manifold configuration. However, branched manifold configuration shows higher pressure drop in spite of enhancements in thermal performance and flow distribution uniformity. Overall performance analysis indicates that RMCHS with branched manifold configuration can be advantageous for high heat flux removal applications if there is no restriction on pumping power requirement.