The Transantarctic Mountains (TAM) are the largest non-compressional mountain belt in the world. Their origin is traditionally related to crustal thickening during the Jurassic Ferrar magmatic event that was followed by episodic uplift in the Early and Late Cretaceous and since the Paleocene. This concept of a long-lived morphological high constitutes a base of virtually all Gondwana reconstructions and global climate models. Here we demonstrate that crossover age relationships between thermochronological (apatite fission track) data and stratigraphic information contradict this established interpretation. Instead these data, together with a wealth of independent thermal indicators and geological evidence require the existence of a vast intra-Gondwana basin between at least Late Triassic and Late Cretaceous times, including during the Ferrar magmatic event. Referred to here as the Mesozoic Victoria Basin (MVB), this basin formed during crustal extension across the paleo-Pacific margin of Antarctica and Australia. Uplift of the TAM with associated basin inversion commenced only with the development of the West Antarctic Rift System in Paleogene times. The recognition of the long-lived MVB has primary consequences for the general understanding of the landscape of Gondwana and the breakup between Antarctica and Australia, West Antarctic rifting and uplift of the TAM, and global long-term climate evolution and faunal radiation.