Flash flooding, a hazard which is triggered by heavy rainfall is a major concern in many regions of the world often with devastating results in mountainous elevated regions. We adapted remote sensing modelling methods to analyse one flood in July 2015, and believe the process can be applicable to other regions in the world. The isolated thunderstorm rainfall occurred in the Chitral River Basin (CRB), which is fed by melting glaciers and snow from the highly elevated Hindu Kush Mountains (Tirick Mir peak’s elevation is 7708 m). The devastating cascade, or domino effect, resulted in a flash flood which destroyed many houses, roads, and bridges and washed out agricultural land. CRB had experienced devastating flood events in the past, but there was no hydraulic modelling and mapping zones available for the entire CRB region. That is why modelling analyses and predictions are important for disaster mitigation activities. For this flash flood event, we developed an integrated methodology for a regional scale flood model that integrates the Tropical Rainfall Measuring Mission (TRMM) satellite, Geographic Information System (GIS), hydrological (HEC-HMS) and hydraulic (HEC-RAS) modelling tools. We collected and use driver discharge and flood depth observation data for five river sub-stream areas, which were acquired in cooperation with the Aga Khan Rural Support Program (AKRSP) organization. This data was used for the model’s calibration and verification. This modelling methodology is applicable for other regional studies especially for rough mountainous areas which lack local observations and river discharge gauges. The results of flood modelling are useful for the development of a regional early flood warning system and flood mitigation in hazardous flood risk areas. The flood simulations and prepared connected video visualization can be used for local communities. This approach is applicable for flood mitigation strategies in other regions.