Performance of a micro-scale heat sink with slip boundary condition at walls is evaluated using entropy generation minimization (EGM) approach. Optimum geometrical parameters and working conditions are obtained by applying two different constraints of fixed microchannel height and constant maximum pressure drop. It has been observed that with fixed channel height constraint, the optimum aspect ratio and Reynolds number are 2.5 and 700, respectively. Slip boundary condition has negligible effect on optimum working parameters while it enhances the thermal performance of the heat sink by almost 4% at fixed height constraint. At maximum pressure drop constraint, the optimum working parameters are aspect ratio of 2.25 and Reynolds number of 850. Slip on the microchannel walls reduces pressure drop and enhances the thermal performance of the heat sink by 11%.