Integrating coastal vegetation into sea dikes is a nature-based approach aimed at combining disaster prevention with ecological sustainability in coastal areas. This study investigates the impact of vegetation on the wave run-up on dikes through numerical analysis. The numerical model used in the study solves the Reynolds-averaged Navier–Stokes equations by adding a vegetation resistance force to account for momentum loss. A stabilized k–ω shear stress transport model considering the vegetation effect was adopted for turbulence closure. A series of numerical simulations was carried out on the wave run-up (Ru) on dikes, focusing on the effects of different vegetation heights, densities, zone lengths, and dike slopes under various wave conditions. The results indicate that vegetation can significantly decrease Ru and may cause the wave to change from breaking to nonbreaking on dikes. The Ru behaviors depend on whether waves break and can be well characterized by the Iribarren number and dimensionless wave momentum flux parameter under breaking and nonbreaking conditions, respectively. Finally, the multivariate non-linear regression (MNLR) and artificial neural network (ANN) methods were adopted to explore a prediction model for evaluating Ru. Comparisons showed that the prediction performance of the ANN model is superior to that of the MNLR model. The ANN model has the potential as a promising predictive tool for obtaining wave run-up on dikes with vegetated foreshores under breaking and nonbreaking conditions.