This study aims at analysing the impact of climate change (CC) on the river hydrology of a complex mountainous river basin—the Budhigandaki River Basin (BRB)—using the Soil and Water Assessment Tool (SWAT) hydrological model that was calibrated and validated in Part I of this research. A relatively new approach of selecting global climate models (GCMs) for each of the two selected RCPs, 4.5 (stabilization scenario) and 8.5 (high emission scenario), representing four extreme cases (warm-wet, cold-wet, warm-dry, and cold-dry conditions), was applied. Future climate data was bias corrected using a quantile mapping method. The bias-corrected GCM data were forced into the SWAT model one at a time to simulate the future flows of BRB for three 30-year time windows: Immediate Future (2021–2050), Mid Future (2046–2075), and Far Future (2070–2099). The projected flows were compared with the corresponding monthly, seasonal, annual, and fractional differences of extreme flows of the simulated baseline period (1983–2012). The results showed that future long-term average annual flows are expected to increase in all climatic conditions for both RCPs compared to the baseline. The range of predicted changes in future monthly, seasonal, and annual flows shows high uncertainty. The comparative frequency analysis of the annual one-day-maximum and -minimum flows shows increased high flows and decreased low flows in the future. These results imply the necessity for design modifications in hydraulic structures as well as the preference of storage over run-of-river water resources development projects in the study basin from the perspective of climate resilience.