The Deep Skull from Niah Cave in Sarawak (Malaysia) is the oldest anatomically modern human recovered from Southeast Asia.For more than 50 years opinions about its relevance to tracing the prehistory of recent people in the region have been in a state of flux. The most widely held view traceable to Brothwell’s initial description and analysis is that the individual is related to Indigenous Australians and provides evidence to support the ‘two-layer’ model of human origins in Southeast Asia. Here we undertake a new assessment of the potential of the Deep Skull to inform these issues and in doing so provide a description of the specimen including a reassessment of its ontogenetic age, sex, morphology and affinities. We find that this individual was most likely to have been of advanced age and a female rather than an adolescent male as originally suggested. We also find that its morphology points towards its affinities being beyond Indigenous Australasians to East Asians. We propose that the Niah individual might best be considered part of a Negrito population that inhabited Borneo during the Pleistocene perhaps establishing their presence in Northern oceanic Southeast Asia by ~36 kyr.