In 1958, Tom Harrisson — curator of the Sarawak Museum, wartime guerrilla commander, and self-taught archaeologist — excavated a human skull from a deep trench in the floor of the Great Cave's West Mouth. The skull, subsequently dated to approximately 37,000–40,000 years BP using radiocarbon methods, was the oldest anatomically modern human remains found in Southeast Asia at that time — a discovery that overturned the prevailing assumption that Homo sapiens arrived in the region only 10,000–15,000 years ago.
Harrisson named his find "the Deep Skull" for the depth at which it was found — roughly 3.4 metres below the cave surface, embedded in the dense organic deposit of layered guano, ash, and sediment that accumulated over millennia. The skull belonged to a young adult, probably in their late teens or early twenties, and the morphology is consistent with modern humans from the tropical SE Asian population — long, low braincase, pronounced cheekbones, and a lightly built face. There is no evidence of burial ritual at this level; the individual may have simply died in the cave.
Above the Deep Skull layer, Harrisson's team found successive cultural strata spanning from approximately 40,000 BP to the ethnographic present: flaked stone tools in the lowest levels; polished stone tools, hand-built pottery, and burial goods from around 4,000 BP; and the boat-coffin burials of the Painted Cave from the last millennium. This stratigraphy makes Niah one of the most complete records of human occupation in Southeast Asia — an archive of over 40,000 years of continuous or semi-continuous habitation in a single site.
More recent dating, using uranium-series methods on associated animal bone and charcoal, has pushed the earliest occupation of the cave back to approximately 60,000 years BP — before the last glacial maximum, when sea levels were 120 metres lower and Borneo was connected to mainland Southeast Asia. The implications are significant: the people who first entered Niah may have arrived via the now-submerged Sundaland landmass, and their descendants include the founders of the earliest known artistic traditions in the region. The park's visitor centre has an exhibition covering the excavation history and key finds.