In this study numerical investigation has been conducted employing pulsating flow in a MicroChannel Heat Sink (MCHS) with phase change material (N-eicosane) as the coolant. The numerical investigation was conducted with H1 boundary condition and laminar pulsating flow condition using commercial software FLUENT. Heat transfer and pressure drop characteristics of the MCHS was calculated for the PCM with different amplitude and frequency of the pulsation and compared with that of the water and PCM under constant velocity flow. Heat transfer performance of the MCHS for both the PCM fluid and water increases for the pulsating flow and it increases with the amplitude of the pulsation; however, pressure drop in case of pulsating flow of PCM fluid remains same compared to the steady flow of PCM. Simulation also has been repeated in this study for two different aspect ratio of the channel.