As well-known, there is not a universal turbulence model that can be used to model all engineering problems. There are specific applications for each turbulence model that make it appropriate to use, and it is vital to select an appropriate model and wall function combination that matches the physics of the problem considered. Therefore, in this study, performance of six well-known Reynolds-Averaged Navier-Stokes (RANS) based turbulence models which are the Standard , the Renormalized Group , the Realizable , the Reynolds Stress Model, the and the Shear Stress Transport and accompanying wall functions which are the standard, the non-equilibrium and the enhanced are evaluated via 3D simulation of a honeycomb heat sink. The CutCell method is used to generate grid for the part including heat sink called test section while a hexahedral mesh is employed to discretize to inlet and outlet sections. A grid convergence study is conducted for verification process while experimental data and well-known correlations are used to validate the numerical results. Prediction of pressure drop along the test section, mean base plate temperature of the heat sink and temperature at the test section outlet are regarded as a measure of the performance of employed models and wall functions. The results indicate that selection of turbulence models and wall functions has a great influence on the results and, therefore, need to be selected carefully. Hydraulic and thermal characteristics of the honeycomb heat sink can be determined in a reasonable accuracy using RANS-based turbulence models provided that a suitable turbulence model and wall function combination is selected.