© 2019, Springer Nature B.V. This study focused on flood damage assessment for future floods under the impact of climate change. Four river basins of Southeast Asia were selected for the study. They included the Pampanga River Basin (PRB) in the Philippines, the Solo River Basin (SRB) in Indonesia, the Lower Mekong River Basin (LMRB) in Cambodia and Vietnam, and the Chao Phraya River Basin (CPRB) in Thailand. Flood damage to rice crops was assessed by flood damage functions considering flood depth and duration and the growth stage of rice plants. Flood characteristics such as flood depth, duration, and distribution were computed using the rainfall–runoff–inundation model to assess flood hazards under the present and future climatic conditions produced by MRI-AGCM3.2S. The damage assessment methodology for rice crops employed in this study was verified using data on past flood events. Then, flood damage assessment was conducted for both the present climate (1979–2003) and future climate (2075–2099) conditions, using MRI-AGCM3.2S precipitation datasets. Flood damage was assessed for worst cases chosen from each climate period and for floods of 50- and 100-year return periods with different rainfall patterns chosen from each climate scenario. The results of flood hazard and damage assessment show that the flood inundation area for a 100-year flood may increase in the future by 20% in PRB; by 66% in SRB; by 27% in LMRB; and by 27% in CPRB. The flood damage area of paddy fields for a 100-year flood may also increase in the future by 16% in PRB; by 55% in SRB; by 23% in LMRB; and by 13% in CPRB.