The northern hopping-mouse (Notomys aquilo) is a cryptic and enigmatic rodent endemic to Australia’s monsoonal tropics. Focusing on the insular population on Groote Eylandt, Northern Territory, we present the first study to successfully use live traps, camera traps and radio-tracking to document the ecology of N. aquilo. Searches for signs of the species, camera trapping, pitfall trapping and spotlighting were conducted across the island during 2012–15. These methods detected the species in three of the 32 locations surveyed. Pitfall traps captured 39 individuals over 7917 trap-nights. Females were significantly longer and heavier, and had better body condition, than males. Breeding occurred throughout the year; however, the greatest influx of juveniles into the population occurred early in the dry season in June and July. Nine individuals radio-tracked in woodland habitat utilised discrete home ranges of 0.39–23.95 ha. All individuals used open microhabitat proportionally more than was available, and there was a strong preference for eucalypt woodland on sandy substrate rather than for adjacent sandstone woodland or acacia shrubland. Camera trapping was more effective than live trapping at estimating abundance and, with the lower effort required to employ this technique, it is recommended for future sampling of the species. Groote Eylandt possibly contains the last populations of N. aquilo, but even there its abundance and distribution have decreased dramatically in surveys over the last several decades. Therefore, we recommend that the species’ conservation status under the Environment Protection and Biodiversity Conservation Act 1999 be changed from ‘vulnerable’ to ‘endangered’.