This study assesses the impact of climate change on flood frequency across seven sites in the Western Cape province of South Africa. The calibrated Water Resources Simulation Model (WRSM)/Pitman hydrological model was run using precipitation inputs from two representative concentration pathways (RCP) scenarios (RCP 4.5 and 8.5) using a combination of eight global circulatory models (GCM) for the two periods (2030–2060 and 2070–2100). GCMs were statistically downscaled using the delta change (DC), linear scaling (LS) and quantile delta mapping (QDM) approaches. Average daily discharge was estimated from each downscaled daily precipitation dataset using the Pitman/WRSM model with the Fuller and Sangal estimation methods used to calculate daily instantaneous peak flows. Flood frequency curves (FFC) were generated using the annual maximum series (AMS) for the GCM ensemble mean and individual GCMs for the return periods between 2 and 100 years. FFCs generated based on LS and QDM downscaling methods were aligned for the GCM ensemble mean in terms of the direction of FFCs. Further analysis was conducted using outputs based on the QDM approach, given its suitability in projecting peak flows. Under this method, both Fuller and Sangal FFCs exhibited a decreasing trend across the Jonkershoek and Little Berg River sites; however, estimated quantiles for low-probability events were higher under the Fuller method. This study noted the variation in FFCs from individual GCMs compared to the FFC representing the GCM ensemble mean. Further research on climate change flood frequency analysis (FFA) in South Africa should incorporate other advanced downscaling and instantaneous peak flow estimation (IPF) methods.