Timor has yielded the earliest evidence for modern humans in Wallacea, but despite its long history of modern human occupation, there is little evidence for human-induced Late Pleistocene extinctions. Here, we report on Late Pleistocene and Holocene bird remains from Jerimalai and Matja Kuru 1, sites that have yielded extensive archaeological sequences dating back to >40 ka. Avian remains are present throughout the sequence, and quails (Phasianidae), buttonquails (Turnicidae) and pigeons (Columbidae) are the most abundant groups. Taphonomic analyses suggest that the majority of bird remains, with the exception of large-bodied pigeons, were accumulated by avian predators, likely the Barn owl Tyto sp. All species represent extant taxa that are still present on Timor today, with the exception of a crane, Grus sp., from the Late Pleistocene of Jerimalai, and a large buttonquail, Turnix sp., from Matja Kuru 1. The crane likely represents an extirpated population of cranes, which were much more widespread throughout the Indonesian archipelago during the Quaternary. The large buttonquail is present at Matja Kuru 1 alongside the extant T. maculosus until at least 1372–1300 cal BP. These two species represent the first records of avian extinctions on Timor. However, a causal relationship between the extinction of these two taxa and human impact cannot be demonstrated at this point.