The subdued topography of the Turkana Depression separates the elevated Ethiopian and Kenyan Plateaus in East Africa. Mechanisms to explain its topography are debated because constraints on upper mantle structure and dynamics are lacking. Attempts to understand the role of the mantle below Turkana in the evolution of rifting between the Main Ethiopian and Southern East African rifts and the onset of Ethiopian Flood Basalt volcanism are also hindered by limited data availability. Here, recently deployed seismic networks in Turkana and neighboring Uganda enable us to develop a new absolute P-wavespeed tomographic model (AFRP21) to image mantle structure below the Turkana depression. Additionally, we use P-to-s receiver functions to map the mantle transition zone (MTZ) discontinuity structure. In the shallow mantle, broadly distributed slow wavespeeds reside below the Main Ethiopian rift. To the south, slow wavespeeds occur in a focused zone below the East African rift, but beneath the northern Turkana depression these are cross-cut by a narrow E-W band of fast wavespeeds. At upper MTZ depths slow wavespeeds are broadly continuous below the East African rift but begin to separate into two distinct anomalies at the base of the MTZ. While receiver functions reveal a broadly thinned MTZ below Cenozoic rift-related magmatism in East Africa, the thinnest transition zone exists below the Turkana Depression. Slow wavespeeds and a thinned MTZ below the Turkana Depression indicate hot upwelling material, thus its low-lying nature is not due to the lack of underlying dynamic support. Instead, the depressed topography may be better explained by Mesozoic-Cenozoic E-W rifting associated with the imaged shallow fast wavespeed band. Furthermore, the main eruptive phase of Ethiopian Flood basalt volcanism may be associated with the African plate’s position over the anomalously thinned MTZ in Turkana at ~30Ma.