The formation of major Palaeoproterozoic and Mesoproterozoic (Cu)-Au deposits at the metal-rich margins of the Gawler Craton, South Australia, has received a lot of attention, however, the relationship between metal occurrences, the exhumation level of the crust and the structural architecture of the craton margins is less clear. Here, we present results from apatite fission track thermochronology applied to basement rocks at the northern margin of the Gawler Craton, revealing a differential cooling history with respect to the Karari shear zone (KSZ). The KSZ is a major shear zone that extends to the Moho in reflection seismic images and has a prolonged history of high-temperature activity during the Paleoproterozoic and Mesoproterozoic. New apatite fission track data show that samples taken to the north of the KSZ record a significant pulse of Carboniferous cooling, in contrast to the Phanerozoic monotonic slow cooling history documented for the area just south of the KSZ. This Carboniferous cooling signal coincides with a sedimentary hiatus between the Neoproterozoic – Devonian Officer Basin and the late Carboniferous to Early Permian Arckaringa Basin, to the north of the KSZ. Therefore, Carboniferous cooling can be linked with exhumation and fault reactivation of the KSZ at that time, which is interpreted to be associated with far-field compression caused by the Alice Springs Orogeny (~450–300 Ma) of central Australia. Following Carboniferous exhumation, a localized thermal overprint was observed in locations associated with Palaeogene palaeochannels.The extent of Phanerozoic exhumation shows a spatial relation with the location of Au (and/or Cu, Fe) mineralization in the northern Gawler Craton. Areas that were significantly modified by Mesoproterozoic mineralizing events, such as the Olympic IOCG province and the Central Gawler Gold Province, record post-Silurian exhumation histories related to the Alice Springs Orogeny. To the west of these two major mineral provinces, Archaean – early Palaeoproterozoic terranes in the northwestern Gawler Craton with abundant Au (and Cu, Fe) mineral occurrences were not affected by Phanerozoic exhumation and denudation. These relations suggest that the Mesoproterozoic mineralized terranes were more susceptible to Phanerozoic deformation compared to the Archaean – Palaeoproterozoic terranes within the stronger parts of the Gawler Craton. Hence, understanding the timing of fault reactivation and the associated relative exhumation level may provide valuable constraints for ore deposit preservation and mineral exploration within the Gawler Craton.