A numerical analysis was performed to evaluate the hydrothermal performance of a pin-fin mini-channel heatsink (MCHS) with six different inlet/outlet flow arrangements from the first and second laws of thermodynamics point of views. The results are presented in terms of several important parameters such as convective heat transfer coefficient (h), CPU mean temperature (Tm, CPU), pumping power (W˙ p), frictional and thermal entropy generation rates (S˙fr and S˙th) as well as Performance Evaluation Criterion (PEC). The results demonstrated that configurations with two inlets and outlets have the lowest W˙ p, S˙fr, h, and highest Tm, CPU among the studied cases. The vorticity intensification is high at the inlet/outlet headers and over the pin-fin bodies for the case with one inlet from the left and two outlets located at opposite sides, namely configuration d. The highest values of S˙fr and h, the lowest value of Tm, CPU, and a moderate value of W˙ p are obtained for configuration d as compared to the other studied cases. In consequence, the maximum PECs (1.61–2.20) is obtained for case d at different Re numbers (500–2000). The PEC of configuration d is nearly 19.77% higher than those of configurations with two inlets and two outlets. Also, the PEC of configuration d is nearly 66.95% higher than those obtained for two other configurations with one inlet and two outlets.