We determined preferences of the Pilliga mouse, Pseudomys pilligaensis, for habitat attributes (ground and vegetation cover) through phases of a population irruption, and characterised refuge sites used when environmental conditions were unfavourable. In general, P. pilligaensis preferred areas with substrate dominated by sand and shrubs rather than rock or litter. However, its habitat selection changed with phases of the irruption. In the Increase phase, it showed no strong habitat preferences, perhaps because the abundance of food (seeds) overrode preferences for more stable habitat values. Its sensitivity to habitat variables increased in the Peak phase. In the Low phase, mice preferred ground cover with higher proportions of sand and shrubs, and lower proportions of rock and litter. Regression analyses suggested that sandy substrate is the most important factor for the refuge habitat of P. pilligaensis, perhaps because a sandy surface can support more understorey shrubs which provide seeds and protection from predators, and provides sites for burrows. Judging from areas where P. pilligaensis was caught during the Low phase, water run-on areas could also characterise refuge habitats. However, further studies are needed to define the species’ refuge habitats fully.