The central rock-rat Zyzomys pedunculatus is categorized as Critically Endangered on the IUCN Red List. Over the last 50 years the species had only been recorded from 14 sites within a 600 km2 area of the West MacDonnell National Park and immediate surroundings in the Northern Territory, Australia. The central rock-rat disappeared from monitoring sites in 2002, coincident with the onset of drought conditions and extensive wildfires. With concern growing for the survival of the species, we sought to locate an extant population. During 2009–2012 we surveyed sites throughout the western sector of the West MacDonnell National Park, including sites where rock-rats had previously been recorded. From a total of 55 sites and 5,000 trap nights we located eight central rock-rats from only five sites (overall detection rate = 0.16 rock-rats per 100 trap nights). All sites were on two mountain-top locations, both of which are over 1,250 m altitude. Evidence of reproductive activity was observed at both locations but the subpopulations were relatively localized and no individuals were captured at any of the sites from which the species was known previous to these surveys. Although the rugged mountains may provide the central rock-rat with some refuge from predation and wildfires, more research is needed to understand better the factors suppressing and constraining the species at the population and landscape scales. Immediate management priorities are prescribed burning to limit the extent and severity of wildfires and trialling a baiting programme with 1080 to target feral cats in the mountains.