Fire regimes are changing throughout the world. Changed fire patterns across northern Australian savannas have been proposed as a factor contributing to recent declines of small- and medium-sized mammals. Despite this, few studies have examined the mechanisms that underpin how species use habitat in fire-affected landscapes. We determined the habitats and resources important to the declining golden-backed tree-rat (Mesembriomys macrurus) in landscapes partially burnt by recent intense fire. We aimed to (i) compare the relative use of rainforest and savanna habitats; (ii) examine the effect of fire history on use of savanna habitats; and (iii) identify key foraging and denning resources. Habitat selection was examined by comparing the availability of eight habitat types around real (used) and generated (available) location points. Individuals used a range of habitats, but consistently selected long unburnt rainforest in preference to recently burnt savanna (1–12 months post-fire); however, recently burnt savanna was used in preference to long unburnt savanna. Tree-rats foraged in Terminalia hadleyana, Planchonia rupestris, Celtis philippensis and Owenia vernicosa, tree species that are found in a variety of habitat types. Individuals used a range of den sites, including cliffs, trees, logs, scree and stags found throughout the study area. Although multiple factors may have led to the decline of Mes. macrurus across its range, these results are consistent with the idea that changes in the savanna structure as a consequence of contemporary fire patterns could also have a role. The continued persistence of Mes. macrurus in the northwest Kimberley may be supported by land management strategies that conserve fruiting and hollow-bearing trees, and maintain the availability of fire-sensitive vegetation types.