The Neptune Range of the Pensacola Mountains, East Antarctica, exposes a record of Early Palaeozoic to Early Mesozoic polyphase deformation along the former East Antarctic margin of Gondwana that is unique within the 3500 km length of the Transantarctic Mountains. The earliest of these orogenic events is the polyphase Early Palaeozoic Ross orogeny. Following two phases of intense pre-late Mid-Cambrian deformation (D1 and D2), a succession of volcanic and sedimentary rocks (sequences 2 and 3) were deposited in late Mid- to Late Cambrian time during a transient period of back-arc rifting. New stratigraphical and structural relationships suggest that the Cambrian succession was deformed during latest Cambrian time while at or near the palaeosurface in a foreland basin setting (D3). D3 deformation is characterized by thrust faulting and folding without the development of a widespread coeval cleavage, with evidence for syntectonic deposition of the basal Neptune Group (sequence 4). The main regional cleavage developed through the Palaeozoic cover rocks (sequences 2–5) is also developed in rare Permo-Carboniferous clastic dykes that cut down through the stratigraphy from the base of the Gale Mudstone. The dyke–cleavage relationship, together with observations of the conglomerate cobbles from throughout the stratigraphical succession, suggests that the most intense deformation within the Cambrian sequences is Permo-Triassic (Gondwanian orogeny) rather than latest Cambrian (late Ross orogeny) as previously concluded. Our data corroborate recent suggestions that the main phase of Ross orogenic deformation is pre-late Mid-Cambrian and not Late Cambrian or Early Ordovician.