Quantifying the thermal histories of rift basins is important for evaluating their resource and CO2 storage potential because temperature controls hydrocarbon generation, and the diagenesis of reservoir rocks. However, in many rift basins, it is difficult to obtain evidence for elevated heat flow accompanying rifting, since paleotemperature data from drilled sections typically record heating related to post-rift burial. Here we integrate geochemical, geophysical and petrophysical data from the Duntroon Sub-basin, Great Australian Bight, that show how strain-migration during multiphase extension can preserve the signature of syn-rift elevated geothermal gradients. During the late Jurassic–early Cretaceous, rifting was focussed along ~ESE-striking normal fault systems in the northern part of the Duntroon Sub-basin. During the late Cretaceous, strain migrated to the southwest through the development of normal faults which accommodated the deposition of Upper Cretaceous strata. The Echidna-1 well was drilled into a basement high, in the footwall of a late Cretaceous fault system, penetrating ~2.5 km of Lower Cretaceous strata. Paleotemperature proxies define an early Cretaceous paleogeothermal gradient of ~60°C km−1, substantially higher than the present-day gradient. Our results indicate that preserved Lower Cretaceous strata were more deeply buried by ~1 km of additional section, which was likely eroded during an episode of mid-Cretaceous exhumation associated with the migrating locus of rifting; this enabled the preservation of thermal signature of elevated syn-rift heat flow. Similar evidence is also observed in the Otway Basin, demonstrating the regional extent of elevated syn-rift heat flow along the southern Australian margin.