In this study, numerical simulations for a single fixed truncated circular cylinder in regular waves were conducted to investigate the nonlinear wave run-up under various dampers and wave period conditions. The present study used the volume of fluid (VOF) technique to capture the air-water interface. The unsteady Reynolds-averaged Navier–Stokes (URANS) equation with the k– ϵ turbulence model was solved using the commercial computational fluid dynamics (CFD) software STAR-CCM+. First, a systematic spatial convergence study was conducted to assess the performance and precision of the present numerical wave tank. The numerical scheme was validated by comparing the numerical results of wave run-up on a bare truncated cylinder with the experimental results, and a good agreement was achieved. Then, a series of parametric studies were carried out to examine the wave run-up time series around the truncated cylinder with single and dual dampers in terms of the first- and second-order harmonic and mean set-up components. Additionally, the local wave field and the flow velocity vectors adjacent to the cylinder were evaluated. It was confirmed that under short wave conditions, the high position of the damper led to a noticeable increase in the wave run-ups with significant changes in the first- and second-order harmonic components.