Alfred Russel Wallace lived for 8 months at Simunjan District with a mining engineer, Robert Coulson, who had explored what is now northern Sarawak for mineral ores.[1] Coulson later wrote to Wallace about finding bones in a number of caves in Sarawak. On further enquiry, Wallace learned that one cave in question "was situated in the district between Sarawak and Bruni (Brunei), on a mountain some distance inland."[2] In March 1864, Wallace favoured Coulson to explore the caves. However, later in May 1864, G. J. Ricketts, a British Consul to Sarawak was appointed to undertake the work. Ricketts did not remain in the post for long and subsequently Alfred Hart Everett was chosen to undertake the work. Everett surveyed 32 caves in three areas, including Niah/Subis (near Miri) and "Upper Sarawak Proper" (to the south of Kuching, near Bau and Lundu areas).[1]

In the 1950s, Tom Harrisson, the curator of Sarawak State Museum was searching for evidence of ancient human activity in Sarawak. He came across Niah Cave, which showed no evidence of ancient human activity in the area. However, he inferred that since the cave was cool and dry and there were millions of bats and swiflets which can be used as food, ancient humans could have lived in the cave. Therefore, in October 1954, Harrisson with his two friends, Michael Tweedie and Hugh Gibb spent two weeks examining the Niah. They found evidence of long term human occupation, habitation, and burial. In 1957, the Sarawak museum organised a larger expedition with transport and equipment from Brunei Shell Petroleum and Sarawak Oilfields Ltd (Shell).[3] Eathernware, shell scrapers, shell ornaments, stone pounders, bone tools, and food remains were found.[3] Radiocarbon dating of the charcoal layers put the site at 40,000 years old, dating back to the Paleolithic era.[3] The expedition team led by Barbara Harrisson discovered the "Deep Skull" in the "Hell Trench" (for its unusually hot condition) at 101 to 110 inches below surface[4] in February 1958.[5] It is a partial skull with maxilla, two molar teeth and a portion of the base of the skull. The skull is highly fragile and is not fossilised. The morphology of the skull is suggestive of belonging to a female in her late teens to mid-twenties. Near the skull, a complete left femur and right proximal tibia were found which belongs to the same individual.[5][6] Tom Harrisson also discovered Neolithic burial sites from 2,500 to 5,000 years ago. The discoveries led to more expeditions in 1959, 1965, and 1972.[5]

In 1960, Don Brothwell concluded that the Deep Skull belonged to an adolescent male who may be closely related to an indigenous Australian from Tasmania.[4] In the 1960s, 122 human remains from Niah were brought to Nevada, United States.[7] There is a lack of paleogeography, stratigraphy, and archeological relationships to support Tom Harrisson's work.[5] Therefore, more fieldwork was conducted by University of Leicester, in collaboration with other universities from Britain, Australia, United States and Sarawak State Museum from 2000 to 2003[8] to establish a more detailed history of Niah Caves.[5] It was known as the "Niah Cave Project".[8] Another dating of the charcoal and the Deep Skull itself was done in 2000.[4] It showed the age of the skeleton to be 37,000 years old.[4] In 2006, studies from the Niah Cave Project found out that the ancient humans living in the Niah Caves probably already used mammal and fish trapping technologies, projectile technology, tuber digging, plant detoxification, and forest burning.[5] In 2013 to 2014, uranium–thorium dating also confirmed the age of the skull.[9] In 2016, further research done by Darren Curnoe noted that the Deep Skull was more resembling of a female adolescent and is more closely resembling the indigenous people of Borneo rather than Tasmanians or the two layer hypothesis which stated that original population of Southeast Asia were emigrated from Australia and later integrated with people from China.[4][9]

In 2010 and 2021, the Sarawak state government nominated the park for an UNESCO's World Heritage Site title.[10][11][12] In 2020, all the 122 pieces of Niah human remains were returned to Sarawak.[13]