The Afar Depression in northeast Africa contains the rift triple-junction between the Nubia, Arabia and Somalia plates. We analyze Rayleigh wave group velocity from 250 regional earthquakes recorded by 40 broadband stations to study the crustal structure across Afar and adjacent plateau regions in northern Ethiopia. The dispersion velocities are inverted to obtain surface wave tomographic maps for periods between 5 and 25 seconds, sensitive to approximately the top 30 km of the lithosphere. The tomographic maps show a significant low dispersion velocity anomaly (>20%) within the upper crust, below the site of recent dyke intrusions (2005–present) in the Dabbahu and Manda-Hararo magmatic segments. Similar low velocity regions are imaged where magma intrusion in the Afar crust has been inferred over the last decade from seismicity or volcanic eruptions. We invert two group velocity curves to compare the S-wave velocity structure of the crust within an active magmatic segment with that of adjacent areas; the active region has a low velocity zone (Vs ∼ 3.2 km/s), between about 6–12 km, which we infer to be due to the presence of partial melt within the lower crust.