The archaeological deposit of cave site Wee Jasper 99 (WJ99), in the foothills of the Namadgi Ranges, spans an uninterrupted 12,000 years beginning in the terminal Pleistocene. Archaeological patterns for the terminal Pleistocene and early Holocene reflect the sparse, short-term occupation seen elsewhere in the region, with a simple lithic technology, and several bone implements reflecting cultural practices involving perishable organic materials. A mid-Holocene phase (7,000 to 4,500 cal BP)—possibly reflecting a small but widespread wave of exploration into the high country—sees increased evidence for site use coinciding with more complex lithic technology, including abundant retouch and backed artefacts. A decrease in cave use follows, perhaps associated with a more general withdrawal of people from high elevations around 4,500 cal BP. The evidence for this latter phase is a reduction in artefact discard and subtle technological changes. In the context of related archaeological records and a local environmental history, the findings contribute to our understanding of the Aboriginal history of the Australian high country and its margins. The unique chronostratigraphy, excellent preservation conditions and abundant unexcavated deposit, establish WJ99 as a regionally important site with high archaeological and palaeoenvironmental research potential.