Animal conservation requires a sound understanding of movement ecology and habitat selection. A key component of this is identifying habitats that animals actively seek or avoid. We quantified habitat selection and investigated the drivers of variability in the short-term activity area of a small, endangered mesopredator, the northern quoll (Dasyurus hallucatus), in the Pilbara region of Western Australia. We collated, standardised, and analysed 14 northern quoll GPS tracking events from four studies conducted between 2014 and 2018. Northern quolls selected activity areas in locations that were more topographically rugged than the broader landscape, characterised by a higher percentage cover of rocky habitat and riverbed, and a lower percentage cover of spinifex sandplain. The size of their activity area also increased with higher percentage cover of non-preferred spinifex sandplain. Therefore, the destruction of habitats preferred by northern quolls - such as mining of rocky habitat - and introduction of structurally simple habitat like spinifex sandplain, is likely to negatively impact resource availability and lead to altered movement patterns that could decrease survival. Future conservation planning should place emphasis on the protection of rugged rocky habitat for northern quolls, as well as efficient movement pathways between patches of this critical habitat.