Phnom Penh, the Capital City of Cambodia, frequently gets flooded when there is heavy precipitation. To this concern, warming temperature and changing precipitation patterns may intensify the situation. This study aimed at (1) assessing the applicability of the urban inundation model of Flo-2D and (2) forecasting inundation characteristics in the downtown area of Phnom Penh under climate change scenario. The selected study area of 12.50 km2 is an independent catchment frequently affected by precipitation-flood events. Also, baseline (2010) and near future (2030s) extreme precipitation events were taken as a case study. The overall model performance was evaluated based on the JICA survey study and flood photo analysis. The result showed that Flo-2D model is applicable in modeling the complex storm drainage in this particular area. Based on the ECHAM4 model under SRES A2, the inundation area will be expanded, and the inundation depth is also expected to increase between 0.20 m and 0.50 m in the near future. This study will provide fruitful information on inundation conditions in the Phnom Penh city, especially most prone and affected areas under future extreme precipitation to local people, researchers, and policymakers to formulate any structural and non-structural adaptation options to overcome the current and future challenges.