Several late-collision and intraplate features are not entirely integrated in the classical plate tectonic model. The Pan-African orogeny (730–550 Ma) in Saharan Africa provides some insight into the contrasting behaviour of cratons and mobile belts. Simple geophysical considerations and geological observations indicate that rigidity and persistence of cratons are linked to the presence of a thick mechanical boundary layer, the upper brittle part of the continental lithospheric mantle, well attached to an ancient weakly radioactive crust. The surrounding Pan-African mobile belts, characterized by a much thinner mechanical boundary layer and more radioactive crust, were the locus of A-type granitoids, volcanism, tectonic reactivation and basin development during the Phanerozoic. During oceanic closures leading to the assembly of Gondwana, lithosphere behaviour was controlled by its mechanical boundary layer, the crust being much less rigid. We suggest that the 5000 km wide Pan-African domain of Saharan Africa, a collage of juvenile and old reactivated basement terranes, has suffered regional continental lithospheric mantle delamination during the early stages of this orogeny, as has been postulated for the more recent Himalayan orogeny in Tibet. Delamination of the continental lithospheric mantle and juxtaposition of crust against hot asthenosphere can explain many features of the late Pan-African (around 600 Ma): reactivation of old terrains, abundant late-tectonic high-K calc-alkaline granitoids, high temperature-low pressure metamorphism, important displacements along mega-shear zones and mantle-derived post-tectonic granitoids linked to a rapid change in mantle source. Recycling into the asthenosphere of large amounts of continental lithospheric mantle delaminated during the Pan-African, can provide one of the reservoirs needed to explain the isotopic compositions of ocean island basalts. Lastly, the lithospheric control over the location of the alkaline rocks enjoins us to consider the thermal boundary layer (the lower ductile part of the continental lithospheric mantle) as a major mixing source zone for these rocks.