The two branches of the East African Rift System (EARS) are believed to have initiated diachronously. However, a growing body of work continues to suggest the onset of rifting in the Western Branch occurred in the Paleogene, coeval to the Eastern Branch. Due to a lack of pre-Miocene stratigraphy, attempts to resolve the geological history of the Western Branch must study the uplift and erosional histories of the modern rift topography. In this study, the rock uplift history of the Rwenzori Mountains, Western Uganda, is resolved to better our understanding of the tectonic history of the Western Branch of the EAR. Through the application of low-temperature thermochronology, χ-mapping and the modelling of river profiles, we show that rock uplift of the Rwenzori dates back to the Oligocene, with thermal history models suggesting uplift induced exhumation may date back as far as the Eocene. This provides tangible evidence that extension began in the region in the Paleogene, coeval with the Eastern Branch, and not the late Neogene. These results have broad implications for the tectonic evolution of the entire East African Rift System and suggest our current understanding of the region's rift history remains incomplete.