The northern East African Rift (EAR) is a unique location where we observe continental rifting in the Main Ethiopian Rift (MER) transitioning to incipient seafloor spreading in Afar. Here we present a 3‐D absolute shear wave velocity model of the crust and uppermost mantle of the northern EAR generated from ambient noise tomography. We generate 4,820 station pair correlation functions, from 170 stations (present over 12 years), which were inverted for phase velocity from 8–33 s period and finally for 3‐D absolute shear velocity structure to 60‐km depth. Everywhere in the uppermost mantle, shear velocity is slower than expected for a mantle peridotite composition (<4.1 km/s). This suggests the presence of pervasive partial melt, with focused upwelling and melt storage beneath the MER, where the slowest velocities (3.20 km/s ± 0.03) are observed. Average crustal shear velocity is faster beneath Afar (3.83 km/s ± 0.04) than the MER (3.60 km/s ± 0.04), albeit Afar has localized slow velocities beneath active volcanic centers. We interpret these slow‐velocity regions (including the MER) as magmatic intrusions and heating of the crust. Beneath the northwestern plateau, crustal velocities are laterally heterogeneous (3.3–3.65 ± 0.05 km/s at 10 km), suggesting a complex geological history and inhomogeneous magma distribution during rift development. Comparison between the MER and Afar allows us to draw conclusions between different stages of rifting. In particular, the MER has the slowest crustal velocities, consistent with longer magma residence times in the crust, early during the breakup process.