Despite the ongoing collapse of native mammal populations across northern Australia, the paucity of robust estimates of population density limits our capacity to identify and understand population change. Here we aimed to provide the first estimates of native mammal density on the Tiwi Islands – one of Australia’s largest remaining refuge areas for native mammals. We conducted intensive live-trapping at four sites that represent varying combinations of fire frequency, feral cat density and feral herbivore presence. We used spatially-explicit capture-recapture models to investigate the density of common brushtail possum (Trichosurus vulpecula) and northern brown bandicoot (Isoodon macrourus). Compared with mainland northern Australia, populations of common brushtail possum and northern brown bandicoot have remained relatively healthy on the Tiwi Islands. Common brushtail possum density was significantly higher on Bathurst Island (1.06 possum ha−1) compared with Melville Island (0.32 possum ha−1), whereas northern brown bandicoot density varied across all four sites (ranging from 0.04 to 0.34 bandicoot ha−1). Unexpectedly, the very frequently burnt Ranku site (Bathurst Island) continues to support healthy populations of both species. These density estimates provide critical information for identifying and understanding future population change for two species that have suffered marked declines across the Australian monsoon tropics. Although the lack of replication limits our ability to draw conclusions regarding the ecological constraints of these mammal populations, our density observations align with a recent conceptual model postulating that the persistence of native mammal populations across northern Australian savannas reflects a complex, but spatially-variable interplay of ‘bottom-up’ and ‘top-down’ processes.