In this research, a Computational Fluid Dynamics (CFD) technique was used to investigate the effect of choking on the flow and heat transfer characteristics of a typical micro-channel heat sink. Numerical simulations have been carried out using Spalart-Allmaras model. Comparison of the numerical results for the heat transfer rate, mass flow rate and Stanton number with the experimental data were conducted. Relatively good agreement was achieved with maximum relative error 16%, and 8% for heat transfer and mass flow rate, respectively. Also, average relative error 9.2% was obtained for the Stanton number in comparison with the experimental values. Although, the results show that the majority of heat was transferred in the entrance region of the channel, but the heat transfer in micro-channels can also be affected by choking at channel exit. Moreover, the results clearly show that, the location where the flow is choked (at the vicinity of the channel exit) is especially important in determining the heat transfer phenomena. It was found that Spalart-Allmaras model is capable to capture the main features of the choked flow. Also, the effects of choking on the main characteristics of the flow was presented and discussed.