This study assessed the impact of climate change on flood frequency and flood source area at basin scale considering Coupled Model Intercomparison Project phase 5 General Circulation Models (CMIP5 GCMs) under two Representative Concentration Pathways (RCP) scenarios (2.6 and 8.5). For this purpose, the Soil and Water Assessment Tool (SWAT) hydrological model was calibrated and validated for the Talar River Basin in northern Iran. Four empirical approaches including the Sangal, Fill–Steiner, Fuller, and Slope-based methods were used to estimate the Instantaneous Peak Flow (IPF) on a daily basis. The calibrated SWAT model was run under the two RCP scenarios using a combination of twenty GCMs from CMIP5 for the near future (2020–2040). To assess the impact of climate change on flood frequency pattern and to quantify the contribution of each subbasin on the total discharge from the Talar River Basin, Flood Frequency Index (FFI) and Subbasin Flood Source Area Index (SFSAI) were used. Results revealed that the projected climate change will likely lead to an average discharge decrease in January, February, and March for both RCPs and an increase in September and October for RCP 8.5. The maximum and minimum temperature will likely increase for all months in the near future. The annual precipitation could increase by more than 20% in the near future. This is likely to lead to an increase of IPF. The results can help managers and policy makers to better define mitigation and adaptation strategies for basins in similar climates.