Previous thermal history models have supported Miocene aged rift initiation of the northern Malawi Rift, but such analysis is lacking from the southern Malawi Rift (which is believed to have initiated at a later time) as are studies assessing interactions of ongoing rifting with the relic of the older late Paleozoic to early Mesozoic Shire Rift just to its south. Here we present new thermal history models derived from new apatite fission-track data from the footwalls of major border faults of the southern Malawi Rift and the Shire Rift. We applied apatite fission track dating to investigate the timing and magnitude of upper crustal (2-5 km; 60 -130 °C) cooling and exhumation ages associated with footwall uplift on 13 rock samples (gneisses, syenite, foliated granite, and granite dikes) collected from the footwall blocks of several major extensional border faults. Mineral separation was undertaken at Zirchron LLC, Geoscience Services using electro pulse disaggregation. The fission track mounting, calibration, and measurement were done at the University of Arizona Fission Track Laboratory. Apatite sample irradiation was carried out at the Oregon State University Radiation Center. The FT ages were measured by using the External Detector Method (EDM) with ages calculated using the zeta calibration of Hurford and Green (1983; doi:10.1016/S0009-2541(83)80026-6) using independent age standards including Durango and Fish Canyon apatite. The lengths of horizontal confined fission tracks were also measured in each of the samples to help constrain the thermal history that most-likely predicts the measured data using inverse thermal modeling software HeFTY version 1.9.3 (Ketcham, 2005; doi:10.2138/rmg.2005.58.11), the apatite FT annealing model of Ketcham et al. (2007; doi:10.2138/am.2007.2281), and Dpar (etch-pit diameter parallel to the c-axis) as an additional kinetic parameter. The timing and rate of rock uplift were further constrained through application of remote sensing fracture strain analyses. These results, when combined with our thermal history modeling results, yield cooling histories that show the border faults of the southern Malawi Rift have likely been active since the early Miocene and that this activity has caused linkage and transfer of strain to the older Shire Rift which appears to have been reactivated and accommodating strain since Pliocene.