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The extents of wave-driven flooding along the coastline fronted by fringing reefs during severe weather depend on the state of the reef. It is believed 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 a better understanding of the impact of climate change on wave-driven flooding hazards over reef-fringed coasts, this study utilized a Boussinesq wave model, FUNWAVE-TVD, to simulate irregular wave transformation and run-up over fringing reefs. Validated with experimental data, the present model shows reasonable prediction of irregular wave evolution and run-up height. 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. Variations of spectral components (i.e., significant sea-swell run-up height, infragravity run-up height and 2% highest run-up height) of irregular wave run-ups were examined and discussed to better understand the underlying physical process.