The global warming trends have accelerated snow and glacier melt in mountainous river basins, which has increased the probability of glacial outburst flooding. Recurrent flood events are a challenge for the developing economy of Pakistan in terms of damage to infrastructure and loss of lives. Flood hazard maps can be used for future flood damage assessment, preparedness, and mitigation. The current study focused on the assessment and mapping of flood-prone areas in small settlements of the major snow- and glacier-fed river basins situated in Hindukush-Karakoram-Himalaya (HKH) under future climate scenarios. The Hydrologic Engineering Center-River Analysis System (HEC-RAS) model was used for flood simulation and mapping. The ALOS 12.5 m Digital Elevation Model (DEM) was used to extract river geometry, and the flows generated in these river basins using RCP scenarios were used as the inflow boundary condition. Severe flooding would inundate an area of ~66%, ~86%, ~37% (under mid-21st century), and an area of ~72%, ~93%, ~59% (under late 21st century RCP 8.5 scenario) in the Chitral, Hunza, and Astore river basins, respectively. There is an urgent need to develop a robust flood mitigation plan for the frequent floods occurring in northern Pakistan.