Liang Bua, a limestone cave on the Indonesian island of Flores, has a depositional sequence that spans the last 95,000 years and includes well-preserved faunal remains. Birds are well represented throughout the stratigraphic sequence at Liang Bua. Here, we present the results of the first comprehensive study of avian remains retrieved from Sector XI, a 2 m by 2 m archaeological excavation along the east wall of the cave. A total of 579 specimens were identified as avian, with 244 belonging to at least 26 non-passerine taxa in 13 families. The late Pleistocene assemblage (23 taxa) includes the first recorded occurrence of vultures in Wallacea, as well as kingfishers, snipes, plovers, parrots, pigeons, and swiftlets. Together, these taxa suggest that during this time the surrounding environment was floristically diverse and included several habitat types. Two of these taxa, the giant marabou Leptoptilos robustus and the vulture Trigonoceps sp., are extinct. Eight taxa were identified in the Holocene assemblage, and five of these were also present in the late Pleistocene. Imperial pigeons Ducula sp. and the Island Collared Dove Streptopelia cf. bitorquata appear only in the Holocene assemblage. The differences in faunal composition between the late Pleistocene and Holocene assemblages may reflect a change in avifaunal composition due to climatic and environmental changes near the Pleistocene–Holocene transition, possibly amplified by impacts associated with the arrival of modern humans; however, the small Holocene sample prevents a firm conclusion about faunal turnover from being made.