We investigated how long-term suppression of populations of a top predator, the dingo Canis dingo, affected composition of sympatric avifauna in Australian deserts, by surveying bird assemblages across ~80 000 km2 of arid dunefields on either side of the Dingo Barrier Fence (DBF; a 5,614 km-long fence separating ecosystems in which dingoes are abundant from ecosystems in which dingoes are functionally extinct). Using fourth-corner modelling, incorporating species’ traits, we identified apparent declines of sedentary birds that nest in low vegetation and small birds that feed primarily on grass seed, and increases in scavenging birds associated with the functional extinction of dingoes. Occupancy differed between sites inside and outside the DBF in 13 bird species. We hypothesise that these differences in bird assemblages across the DBF result, in part, from increases in kangaroos (Macropus spp.) and red foxes (Vulpes vulpes) in arid landscapes where dingoes have been removed. Our study provides evidence that the functional extinction of a large terrestrial predator has had pervasive ecosystem effects, including shifts in composition of avian assemblages.