Moving into montane rainforests was a unique behavioural innovation developed by Pleistocene Homo sapiens as they expanded out of Africa and through Southeast Asia and Sahul for the first time. However, faunal sequences from these environments that shed light on past hunting practices are rare. In this paper we assess zooarchaeological evidence from Yuku and Kiowa, two sites that span that Pleistocene to Holocene boundary in the New Guinea Highlands. We present new AMS radiocarbon dates and a revision of the stratigraphic sequences for these sites, and examine millennial-scale changes to vertebrate faunal composition based on NISP, MNI, and linear morphometric data to shed light on variability in hunting practices, processes of natural cave deposition, and the local palaeoenvironment at the end of the LGM through to the Late Holocene. We show that Yuku was first occupied at least c. 17,500 years ago and that Late Pleistocene–Early Holocene hunters targeted a wide range of small-bodied and agile species from the mid-montane forest, with a particular focus on cuscus (Phalanger spp.). At Kiowa, occupied from around 12,000 years ago, a similar range of species were targeted, but with an added emphasis on specialised Dobsonia magna fruit bat hunting. We then integrate other zooarchaeological data from the wider Highlands zone to build a model of generalist-specialist hunting dynamics and examine how this more broadly contributes to our understanding of tropical foraging during the Late Pleistocene and Holocene.