Extreme precipitation and associated flooding cause severe damage to society and the environment. Future climate projections suggest an intensification of precipitation extremes in many regions. However, there is an increasing need for climate change impact assessment at higher spatial resolution, particularly for regions with complex geography such as Southeast Asia (SEA). In this study, we analysed the NASA Earth Exchange 0.25° resolution daily precipitation projections from an ensemble of 20 climate models under two emission scenarios RCP4.5 and RCP8.5. The variability in future precipitation projections is analysed and quantified for six geographical subregions, two climatological regions (wet and dry), and the low‐elevation coastal zones in SEA. Various aspects of precipitation structure are studied using indices that characterize precipitation amount, number of heavy precipitation days, extreme precipitation amount, and maximum daily precipitation at annual and seasonal scales. The results show substantial increases in mean and extreme precipitation in many parts of SEA by the end of the 21st century under both emission scenarios, thus increasing the region's vulnerability to precipitation‐driven hazards. The projected centennial increase in total annual precipitation relative to the baseline period of 1970–1999 when averaged over all land grid cells is about 15% under RCP8.5 scenario, with larger values (∼20%) over mainland SEA and Philippines and smaller values (∼6%) in Java island. The projected changes in extreme precipitation are stronger compared to the total annual precipitation under both emission scenarios. The New Guinea and Java regions show the largest and smallest increases in annual maximum daily precipitation, with ensemble mean values of 30 and 17%, respectively, under RCP8.5 scenario. The results also reveal large inter‐model spread in projected changes, particularly during boreal winter and summer months.