Modelling the occupancy of species is a key part of the discipline of ecology, with particular efforts often focused on identifying which environmental, vegetation and other factors influence why a given species occurs where it does. Here, based on data gathered between 2003 and 2016, we developed models of the environmental, terrain and vegetation factors associated with site occupancy of the Southern Long‐nosed Bandicoot (Perameles nasuta Geoffroy) at Booderee National Park in the Jervis Bay Territory, south‐eastern Australia. The Long‐nosed Bandicoot is a nocturnal omnivorous marsupial which feeds primarily on subterranean invertebrates and fungi. The species has undergone a major reduction in abundance and site occupancy following a peak irruption in 2006 with the percentage of the sites at which the species was present declining from 74.3% of sites trapped in 2006 to 10.5% of sites trapped in 2016. We found the Long‐nosed Bandicoot was distributed widely across Booderee National Park and occurred in all six broad vegetation types in the reserve (forest, heathland, woodland, shrubland, sedgeland and rainforest). Detection‐occupancy modelling revealed that the persistence and colonisation of sites by the species were negatively associated with the per cent cover of leaf litter, irrespective of broad vegetation type. Occupancy models are an important tool in identifying parts of landscapes most likely to support populations of particular species, such as the Long‐nosed Bandicoot over time, and they may assist management of protected areas to prioritise resources to manage the habitat of those areas.