Introduced species can cause major disruptions to ecosystems, particularly on islands. On Christmas Island, the invasive yellow crazy ant (Anoplolepis gracilipes) has detrimental impacts on many animals ranging from the iconic red crabs (Gecarcoidea natalis) to the Christmas Island Thrush (Turdus poliocephalus erythropleurus). However, the full extent of its effects on the island’s fauna is not yet known. In this study, we investigated the impact of the yellow crazy ants on the island’s last native mammal: the Christmas Island flying-fox (Pteropus natalis). This species has been described as a keystone species, but has recently experienced substantial population decline to the extent that it is now listed as critically endangered. We examined the impacts of the yellow crazy ants on the roosting behaviour of the Christmas Island flying-fox, and on its local and island-wide distribution patterns. We showed that the crazy ants increased behaviours in the flying-foxes that were associated with avoidance of noxious stimuli, and decreased behaviours associated with resting. Roost tree selection and roost site location were not related to variation in the abundance of crazy ants on the island. Our results indicate that the crazy ants interfere with the activity budgets of the flying-foxes. However, the flying-foxes failed to relocate to ant-free roost trees or roost sites when confronted with the noxious ant, suggesting that the flying-foxes are either not sufficiently disturbed to override strong cultural attachment to roosts, or, are behaving maladaptively due to ecological naïveté.