Beneath sub-equatorial Africa, there is convincing evidence for a gigantic, slow, velocity anomaly within the lower mantle that is inferred to be a thermochemical superplume. Here, we define the spatial and temporal pattern of uplift across the northern edge of this putative superplume by analyzing stratal geometries and stacking velocities of Neogene sedimentary rocks. These marine deposits are imaged on a dense grid of seismic reflection profiles that straddle the southwest African coastal shelf. Inverse modeling of stacking velocity profiles demonstrates that there have been at least two significant phases of uplift. A post-Pliocene uplift event increases from 0 to ~500 m elevation over a distance of ~1000 km, in close agreement with geophysical estimates of the present-day variation of dynamic topography. An earlier phase of uplift occurred in middle Oligocene time (ca. 30–35 Ma ago). We propose a two-stage development of epeirogeny in which a Middle Oligocene phase of uplift may be related to initiation and growth of the African superplume. Post-Pliocene denudation records rapid (100–250 m/Ma) vertical motions generated by upper mantle convection, which vary on length scales of 500–1000 km. Our results support the existence of a convective circulation system that has operated on different temporal and spatial scales beneath the African plate.