We investigate the upper crustal velocity structure beneath the Rwenzori Mountains in western Uganda. This mountain range of nonvolcanic origin is situated within the western branch of the East African rift and reaches altitudes of more than 5000 m. The cause for the extreme uplift within a rifting environment is currently being debated. The local tomographic inversion described here is based on 2053 earthquakes recorded by a network of up to 35 stations covering an area of 140×90 km2. The deployment was limited by the international border between Uganda and the Democratic Republic of the Congo, such that a number of recorded events lie outside the station perimeter. We perform synthetic tests to assess the effect of location uncertainty on the results. The tests show that the resolution is good between 3 and 15 km depth within a restricted area covered by the array. However, smearing can be significant in some parts. The inversion for P- and S-wave velocity anomalies is performed independently and agrees well. The interpretation of the results is based on a synthetic model that reproduces the same pattern of anomalies as that obtained after inversion of the real data. Our models exhibit a significant negative velocity anomaly (up to -8%) beneath the central Rwenzori Mountains. This could be an indication for active magmatic intrusions beneath the mountains in relation to the rifting. The presence of low velocities in the northwest of the range, within the rift, may be related to magmatic processes beneath the Buranga hot springs. Higher velocities are found elsewhere beneath the eastern rift shoulder and are thought to be related to old cratonic crust.