Deep seismic reflection imaging combined with geochronological, palaeomagnetic and stratigraphic data indicate that the world class sediment-hosted Pb–Zn deposits of northern Australia are preferentially concentrated in the post-extensional syn-inversion fraction of the Calvert and Isa superbasins. These fractions were deposited at 1650–1640 Ma and 1615–1575 Ma respectively, and overlap the age of known orogenic events in both Australia and western Laurentia, pointing to a common origin linked to crustal shortening and supercontinent assembly. Crustal shortening resulted in thrust faulting and reactivation of earlier-formed extensional faults leading to upward expulsion of mineralizing fluids at or close to the seafloor while basin inversion and sedimentation were still in progress. This is contrary to most existing models for Pb–Zn ore genesis in northern Australia where fluid flow and mineralization have been attributed to syn-extensional processes accompanying continental breakup or thermal sag. Instead, mineralization post-dates passive margin formation and more probably occurred in a contractional or foreland basin setting involving orogenic loading of the continental crust from the east during assembly or reassembly of the Nuna supercontinent. A strikingly similar history of basin inversion and Pb–Zn mineralisation is shared by the late Neoproterozoic-early Paleozoic Selwyn and older epicratonic basins of western North America.