East Antarctica remains one of the few continental regions on Earth where an understanding of the origin and causal processes responsible for topographic relief is largely missing. Low-temperature thermochronology studies of exposed Precambrian basement revealed discrete episodes of cooling and denudation during the Paleozoic–Mesozoic; however, the significance of these thermal events and their relationship to topography across the continental interior remains unclear. Here we use zircon and apatite (U-Th)/He thermochronology to resolve the low-temperature thermal evolution of a poorly exposed section of East Antarctic basement in the Bunger Hills region and gain insights into the chronology and style of landscape evolution across East Antarctica. Thermal history modeling results indicate that Precambrian basement in the Bunger Hills region experienced a distinct cooling episode during the Late Paleozoic–Triassic, which we relate to ~2–4 km of regional exhumation associated with intracontinental rifting, followed by a second episode of localized cooling and ≤1 km exhumation during the Late Jurassic–Cretaceous separation of India from East Gondwana. These findings, combined with existing thermochronological and tectonic evidence, support a continent-scale denudation event associated with uplift and exhumation of large sections of Precambrian basement during Late Paleozoic–Triassic Pangea-wide intracontinental extension. By contrast, continental extension associated with the Jurassic–Cretaceous breakup of East Gondwana resulted in significant denudation only locally in regions west of the Bunger Hills. We propose that the combined effects of these Paleozoic–Mesozoic tectonic events had a profound impact on the topography across the East Antarctic interior and influenced the long-term landscape evolution of East Antarctica.