The hydrological extremes like floods and drought are increasing in recent decades all over the world but particularly in South Asia. Pakistan ranked 5th most vulnerable as per the climate risk index because it is susceptible to floods and droughts across various spaces and times. The recent evidence of climate change led us to study the floods for a high-altitude river basin, the Kabul River basin (KRB), Pakistan. The region is customarily influenced by flooding. Accordingly, the study was planned to examine the most likely impact of climate change on extreme floods under high-end warming scenario RCP 8.5. The multi-model ensemble from CMIP5 along with HEC-HMS was employed to quantify the impact of climate change on extreme floods. The main research results represented that the projected flood magnitude has been decreased in the future period (2016–2100) as compared to the historical period (1981–2015), for the Kabul River at Nowshera under RCP 8.5. The floods of 2, 5, 10, 25, 50, and 100 years are projected to be decreased by 2%, 24%, 23%, 16%, 11%, and 17% respectively. The magnitude of 3-day rainfall events of all durations is projected to decrease throughout the basin. Therefore, the corresponding magnitude of extreme flood events will also decrease in the KRB, Pakistan. However, the frequency of the 3-day rainfall events of 2, 5, and 10 years return period has been increased in the future period (2016–2100) as compared to the historical period (1981–2015). This frequent occurrence of extreme rainfall events can be challenging to mitigate the flood hazard. The findings of the study will be vital to improving flood management under changing climate in the region.