The re-excavation of Karnatukul (Serpent’s Glen) has provided evidence for the human occupation of the Australian Western Desert to before 47,830 cal. BP (modelled median age). This new sequence is 20,000 years older than the previous known age for occupation at this site. Re-excavation of Karnatukul aimed to contextualise the site’s painted art assemblage. We report on analyses of assemblages of stone artefacts and pigment art, pigment fragments, anthracology, new radiocarbon dates and detailed sediment analyses. Combined these add significantly to our understanding of this earliest occupation of Australia’s Western Desert. The large lithic assemblage of over 25,000 artefacts includes a symmetrical geometric backed artefact dated to 45,570–41,650 cal. BP. The assemblage includes other evidence for hafting technology in its earliest phase of occupation. This research recalibrates the earliest Pleistocene occupation of Australia’s desert core and confirms that people remained in this part of the arid zone during the Last Glacial Maximum. Changes in occupation intensity are demonstrated throughout the sequence: at the late Pleistocene/ Holocene transition, the mid-Holocene and then during the last millennium. Karnatukul documents intensive site use with a range of occupation activities and different signalling behaviours during the last 1,000 years. This correlation of rock art and occupation evidence refines our understanding of how Western Desert peoples have inscribed their landscapes in the recent past, while the newly described occupation sequence highlights the dynamic adaptive culture of the first Australians, supporting arguments for their rapid very early migration from the coasts and northern tropics throughout the arid interior of the continent.