The great desert skink (Liopholis kintorei) of the Egerniinae subfamily (Reptilia: Scincidae) is a communal burrowing lizard that inhabits arid spinifex grasslands in central Australia. Great Desert Skink activity is centred in and around the burrows which are inhabited for many years. However, it is not known whether skinks select burrow sites with specific attributes or how continuing occupancy of burrows is influenced by the surrounding habitat; especially post-fire, when plant cover is reduced. Here we test whether great desert skink burrows in areas burnt two years previously and in longer unburnt areas are associated with particular habitat attributes, and whether there are differences between occupied and recently abandoned burrow sites. Vegetation composition, cover and surface soil characteristics at 56 established great desert skink burrows, including occupied and recently unoccupied burrows, were compared with 56 random nearby non-burrow control sites. Burrow sites had higher plant cover compared with the surrounding landscape in both recently burnt and longer unburnt areas and were more likely to be associated with the presence of shrubs. Soil stability and infiltration were also higher at burrow sites. However we found no evidence that burrows with lower cover were more likely to be abandoned. Our results suggest that great desert skinks may actively select high cover areas for burrow construction, although differences between burrow and control sites may also partly reflect local changes to plant cover and composition and soil properties resulting from burrow construction and long term habitation of a site. Further research should determine if burrows with shrubs or higher plant cover provide greater protection from predators, more structural stability for burrow construction, increased prey abundance or other benefits. We recommend that maintenance of areas with relatively higher plant cover be prioritised when managing great desert skink habitat.