Wave hydrodynamics over fringing reefs is largely controlled by the reef surface roughness and hydrodynamicforcing. It is believed that climate change will result in a net increase in the water depth over the reef flat, a degrading of the surface roughness of coral reefs and changes in extreme incident wave heights. For an accurate assessment of how climate change affects the safety of reef-fringed coasts, a numerical study of the impact of climate change on irregular wave run-up over reef-fringed coasts was carried out based on a Boussinesq wave model, FUNWAVE-TVD. Validated with experimental data, the present model shows reasonable prediction of irregular wave evolution and run-up height over fringing reefs. Numerical experiments were then implemented based on the anticipated effects of climate change and carried out to investigate the effects of sea level rise, degrading of the reef surface roughness and increase of extreme incident wave height on the irregular wave run-up height over the back-reef beach respectively. Variations of run-up components (i.e., spectral characteristics of run-up and mean water level) were examined specifically and discussed to better understand the influencing mechanism of each climate change-related effect on the run-up.