Humans have influenced island biotas in the last few millennia through widespread forest clearances and the introduction of commensals and pest species, causing the extinction of island endemics around the world. This is particularly evident in Timor, where more than 40,000 years of human habitation produced few if any extinctions until the last few thousand years when Timor lost most of its endemic murids. We present new records and dates for endemic rodents and introduced fauna from archaeological cave deposits in Timor-Leste that captures this human-mediated transition. We discuss the chronology of faunal introductions and losses at these sites, and compare the Timor records to other records in surrounding islands. We find no directly dated evidence for significant overlap between the introduction of exotics and extinction of murid endemics at ecological timescales, although determining true extinction and introduction ages will require direct dating and modelling of taxon occurrences, which may bring extinction and introduction closer together in time. Nevertheless, we suggest that, based on current data, the almost complete loss of Timor’s endemic forests were the primary driving force in rodent extinctions.