Our study builds on recent research on the role of drought refuges in facilitating the persistence of arid-dwelling rodents during extended dry periods by characterizing the spatial ecology and shelter use of the plains mouse, Pseudomys australis, a threatened Australian desert rodent that uses refuges. We radiotracked 18 P. australis in the western Simpson Desert, Australia, during November 2014 and May 2015, when individuals were expected to be confined to cracking clay refuge habitat. We also measured the dimensions (length, width, and perceived vertical depth) of shelter sites used by tracked individuals. A sufficient number of fixes (range = 17–64) for home range calculation by kernel density estimation was obtained for 11 of the 18 tracked individuals. Total ranges were calculated at the 90% isopleth and core areas at the 50% isopleth. The tracked animals occupied small home ranges (1.35 ± 0.56 ha) within cracking clay refuge habitat for the duration of the study. Individuals occupied distinct core areas, which were just 22.57 ± 1.54% the area of the total home ranges and centered on 1–2 frequently used burrows. Overlaps in total ranges and some burrow sharing were observed between neighboring individuals; however, core areas overlapped between only 1 pair of animals, suggesting that some group structuring may occur in P. australis refuge populations. Cracks used by tracked individuals were wider and deeper than burrows. Our study found that the short-term home ranges of the radiotracked P. australis during a dry period were situated entirely within cracking clay refuge habitat, and that shelter resources, and potentially social structuring, influence the use of space by this species.