In computational fluid dynamics (CFD) simulations of internal combustion engines, one of the critical modeling parameters is the valve setup. A standard workaround is to keep the valve opens at a certain clearance (minimum valve lift), while imposing a solid boundary to mimic valve closure. This method would yield a step change in valve lift during opening and closing event, and different valve event timing than hardware. Two parametric studies were performed to examine (a) the effect of the minimum valve lift and (b) the effect of grid resolution at the minimum valve lift on predicted in-cylinder flow fields in Reynolds-averaged Navier–Stokes (RANS) simulations. The simulation results were compared with the state-of-the-art particle image velocimetry (PIV) measurement from a two-valve transparent combustion chamber (TCC-3) engine. The comparisons revealed that the accuracy of flow simulation is sensitive to the choice of minimum valve lift and grid resolution in the valve seat region. In particular, the predicted in-cylinder flow field during the intake process was found to be very sensitive to the valve setup. A best practice CFD valve setup strategy is proposed as a result of these parametric studies. The proposed CFD valve setup was applied to large eddy simulation (LES) of TCC-3 engine and preliminary results showed noticeable improvement already. Further evaluation of the valve setup strategy for LES simulations is ongoing and will be reported in a separate report.