The analysis of numerous apatite fission track (AFT) data sets throughout the Transantarctic Mountains reveals three episodes of upper crustal cooling since the Cretaceous. Traditional thinking presumes that this cooling was produced by uplift and denudation stages occurring in the Early Cretaceous, the Late Cretaceous, and the Cenozoic. However, diachronous paleotemperatures up to 400°C determined on Jurassic superficial rocks require substantial burial and thermal activity before a stable geothermal gradient was established during the Late Cretaceous. Therefore, an extensive sedimentary basin between Antarctica and Australia must have existed, likely due to continental rifting processes leading to Gondwana breakup and passive margin formation. Denudation-dominated cooling occurred only with the formation of the Cenozoic West Antarctic Rift System and the related uplift of the Transantarctic Mountains since ca. 55 Ma.