In this study, simulations over Southeast Asia (15°S–40°N, 80°–145°E) at 36 km resolution were conducted for the period 1989–2007 using the Regional Climate Model version 4.3 (RegCM4.3) under the framework of the Southeast Asia Regional Climate Downscaling/Coordinated Regional Climate Downscaling Experiment – Southeast Asia (or SEACLID/CORDEX-SEA) project. Forced by the European Centre for Medium-Range Weather Forecasts (ECMWF) Interim Reanalysis (ERA-Interim), 18 experiments were carried out using different combinations of cumulus parameterization and ocean flux schemes. Twelve extreme indices for both rainfall and temperature were estimated from the model output. A statistical omega index was used to measure the degree of similarity among the 18 experiments in phase and shape. The results showed relatively high similarities among the experiments over mainland Asia compared to those over the Maritime Continent for both seasonal and inter-annual variability. The extreme rainfall indices had a lower omega compared to that of temperature. Observed daily rainfall and temperature data at 52 meteorological stations over the SEA region were used to validate the simulated extreme indices. The results showed that extreme temperature indices were generally underestimated across the region. Systematic biases for each simulated rainfall index were also identified. A score ranking system was established to compare the relative performance of the 18 experiments over the 52 selected stations objectively. It was shown that the experiments with the Massachusetts Institute of Technology (MIT)-Emanuel scheme performed relatively better than the other convective schemes. The combination of the MIT-Emanuel convective scheme with the Biosphere–Atmosphere Transfer scheme (BATS1e) ocean flux scheme produced the best performance.