Models of continental breakup remain uncertain because of a lack of knowledge of strain accommodation immediately before breakup. Our new three-dimensional seismic velocity model from the Main Ethiopian rift clearly images mid-crustal intrusions in this active, transitional rift setting, supporting breakup models based on dike intrusion and magma supply. The most striking features of our velocity model are anomalously fast, elongate bodies (velocity, Vp ∼6.5–6.8 km/s) extending along the rift axis, interpreted as cooled mafic intrusions. These 20-km-wide and 50-km-long bodies are separated and laterally offset from one another in a right-stepping en echelon pattern, approximately mimicking surface segmentation of Quaternary volcanic centers. Our crustal velocity model, combined with results from geologic studies, indicates that below a depth of ∼7 km extension is controlled by magmatic intrusion in a ductile middle to lower crust, whereas normal faulting and dike intrusion in a narrow zone in the center of the rift valley control extension in the brittle upper crust. This zone is inferred to be the protoridge axis for future seafloor spreading.