Abstract In transboundary river basins, climate change is being considered as a concern of higher degree than it is in other parts of the world. The Kabul River Basin, a sub-basin of the Indus River system shared by Pakistan and Afghanistan, is no exception. High level of sensitivity of its flow to temperature makes it imperative to analyse climate change impacts on the flow regime of this important river for efficient water resources management on both sides of the border. The snowmelt runoff model integrated with remote sensing snow cover product MODIS was selected to simulate daily discharges. Future projections were generated for two selected time slices, 2011–2030 (near future) and 2031–2050 (far future), based on output of an ensemble of four GCMs' RCP 4.5 and RCP 8.5 scenarios. Analysis shows a significant temperature increase under both scenarios in the near and far future at a high-altitude region of the basin which mostly receives snowfall that is also found increasing over time. Consequently, it causes a change in the flow regime and more frequent and heavier flooding events, thus calling for a joint strategy of the two riparian countries to mitigate the anticipated impacts in the basin for safety of people and overall prosperity.