40Ar/39Ar systematics within metasedimentary rocks exposed in the southern Prince Charles Mountains, East Antarctica, were thermally reset during a period of Early Palaeozoic (between 524 ± 1 Ma and 486 ± 2 Ma) orogenesis. This event affected three temporally distinct (Archaean to Neoproterozoic) stratigraphic levels that are now exposed in the upper crust. In the structural record, evidence of orogenesis during Early Palaeozoic times is preserved as late-stage, subvertical mylonite zones in the Archaean orthogneiss–metasedimentary basement and thin-skinned folding and thrusting of the overlying Neoproterozoic metasedimentary rocks. Synchronous cooling ages, contrasting structural styles and similar peak metamorphic conditions are interpreted as reflecting basement-involved thin-skinned deformation that was the result of inversion of a Neoproterozoic basin. The presence of pre-existing crustal heterogeneities is the mechanism that localized Early Palaeozoic orogenesis within the region. This interpretation differs from previous models that attribute Early Palaeozoic orogenesis within the southern Prince Charles Mountains to a collisional tectonic setting. An Early Palaeozoic intra-cratonic setting for the region suggests that amalgamation between India and Antarctica was likely to have occurred prior to the final construction of Gondwana.