Abstract The Rwenzori region, which is located between the Democratic Republic of Congo and Uganda, is part of the western branch of the East African Rift. With elevations of c. 5000 m a.s.l., the Rwenzori Mountains are situated between the Albert Rift and the Edward Rift segments and cover an area of approximately 120 km by 50 km. In this study we investigate the Moho topography beneath the Rwenzori region based on data from a network of 33 broadband seismic stations that were operated from September 2009 until August 2011. Variations of crustal thickness are obtained from the H-κ stacking method applied to P-receiver functions. We discuss the effect of low velocity layers within the crust on the determined Moho depths, which range from 20 km up to 39 km. The lack of a crustal root beneath the Rwenzori Mountains and its location in an extensional setting are contrary to the orogenesis generated by collisions of tectonic units. Our results indicate crustal thinning and provide evidence for the alternative mechanism of crustal bending, triggered by the tensile stress and the elasticity of the crust. Supplementary material: Examples and methods for identifying crustal structures and sediment layers are available at http://www.geolsoc.org.uk/SUP18801 .