In this paper, we present a conceptual model to describe the post‐Pan‐African (<∼500 Ma) basement cooling pattern for NE Mozambique. The cooling history is derived from combined low‐temperature thermochronological dating methods comprising titanite, zircon and apatite fission track data. After Pan‐African orogenesis (∼620–530 Ma) the Precambrian basement was subject to extensional tectonics and a relatively slow Lower Ordovician to Recent cooling with rates of ∼2.2°C to 0.1°C Myr⁻¹. Basement rock cooling was mainly a response to Late Paleozoic to Mesozoic rifting between northern Mozambique and East Gondwana during the opening of the Rovuma and Mozambique sedimentary basins. Meanwhile, different dynamic margin and basin types evolved along the eastern and southern continental margins of NE Mozambique. During the Late Carboniferous–Triassic an intracontinental rift opened between NE Mozambique and East Antarctica, and the fastest denudation was focused along the present southern continental margin. Since the Middle Jurassic, tectonic denudation along the Rovuma margin was localized in a narrow zone, some 30 km wide, associated with erosion along strike‐slip faults. In contrast, the Jurassic‐Cretaceous opening and ocean crust formation in the Mozambique Basin were accompanied with an unusually uniform Late Cretaceous cooling pattern over a large area (∼150,000 km²) of the basin hinterland. This pattern can be explained by isostatic and erosional response to magmatic underplating or differential stretching, whereby the old Pan‐African lithospheric structure appears to have important controls on later events.