In this paper, a 3D-conjugated heat transfer model for nano-encapsulated phase change materials (NEPCMs) cooled micro pin fin heat sink (MPFHS) is presented. The governing equations of flow and heat transfer are solved using a finite volume method based on collocated grid and the results are validated with the available data reported in the literature. The effect of nanoparticles volume fraction (C = 0.1, 0.2, and 0.3), inlet velocity (Vin = 0.015, 0.030, and 0.045 m/s), and bottom wall temperature (Twall = 299.15, 303.15, 315.15, and 350.15 K) is studied on Nusselt and Euler numbers as well as temperature contours in the system. The results indicate that significant heat transfer enhancement is achieved when using the NEPCM slurry as an advanced coolant. The maximum Nusselt number when NEPCM slurry (C = 0.3) with Vin = 0.015, 0.030, and 0.045 (m/s) is employed is 2.27, 1.81, and 1.56 times higher than the ones with base fluid, respectively. However, with increasing bottom wall temperature, the Nusselt number first increases then decreases. The former is due to higher heat transfer capability of coolant at temperatures over the melting range of phase change material (PCM) particles due to partial melting of nanoparticles in this range. However, the latter phenomenon is due to the lower capability of the NEPCM particles and consequently coolant in absorbing heat at coolant temperatures is higher than the temperature correspond to fully melted NEPCM. It was observed that the NEPCM slurry has a drastic effect on the Euler number, and with increasing volume fraction and decreasing inlet velocity, the Euler number increases accordingly.