Ambient noise tomography has been used to construct Rayleigh-wave group velocity maps covering the northern (NMER), central (CMER) and southern (SMER) parts of the Main Ethiopian Rift (MER). In addition, dispersion curves, extracted from the group velocity maps, have been inverted to obtain a quasi-3-D model of crustal shear wave velocities. In comparison to crustal structure on the Ethiopian Plateau, we find (1) lower shear wave velocities at all crustal depths beneath the Yerer-Tullu Wellel Volcanotectonic Lineament, (2) lower shear wave velocities throughout the MER at upper crustal depths (<10 km), (3) regions of lower shear wave velocities at mid- (10–20 km) crustal depths beneath the Wonji Fault Belt (WFB), in the transition between the NMER and CMER, and beneath the Silti-Debre zeit Fault Zone (SDFZ) on the western side of the CMER, (4) an offset in the velocity pattern at mid-crustal depths between the NMER and CMER coincident with the Boru-Toru Structural High (BTSH) and (5) little evidence for lower shear wave velocities at mid- or lower-crustal depths beneath the SMER. We attribute these findings primarily to along-strike changes in crustal composition, melt content and thermal structure resulting from the Cenozoic to recent magmatism, and also, at upper crustal depths (<10 km), to basin structure and fill. Our findings corroborate a magmatic plumbing model for the MER that shows two major zones of magmatic activity, one beneath the WFB and the other beneath the SDFZ. The shear wave velocity patterns in our model show good correlation with the depth extent of seismicity, upper-mantle seismic anomalies and seismic anisotropy, as would be expected if the along-strike changes in shear wave velocity reflect the thermal and compositional structure of the crust.