Low-temperature thermochronology studies record Miocene aged rift initiation of the northern Malawi Rift. However, no studies are available from the southern Malawi Rift and the Shire Rift, which are thought to have initiated at a later time. Here we present thermal history models derived from new apatite fission-track and (U-Th)/He data from the footwalls of major border faults of the southern Malawi Rift, that reveal three distinct cooling episodes in the Cretaceous, Eocene–Oligocene, and Late Oligocene–Pliocene. These results suggest that the southern Malawi Rift has been accommodating strain along its border faults since the Miocene, just as in the northern Malawi Rift. The timing and rate of extensional strain was further constrained through the application of remote sensing. These results, when combined with our thermal history modeling, yield inferred deformation strain rates that support linkage between the modern Malawi Rift and the older Shire Rift. Cooling histories show that the border faults of the southern Malawi Rift have likely been active since the Late Oligocene - Early Miocene and that this activity has caused linkage and transfer of strain to the older Shire Rift which our results suggest to have been reactivated since the Miocene too. These results provide evidence of the coeval onset of extension along the full length of Malawi Rift and possibly the Western Branch of the East African Rift System.