This rat exists in a complex burrow system with multiple entrances and several nesting chambers. In Namaqualand, the burrows were found to occupy an average of 73 m2 (786 sq ft) and average 93 entrances. This multiplicity of entrances, some in the open and some in concealed locations, help the diurnal rodent to take cover rapidly when predators threaten. On spotting a potential danger, a high-pitched whistling warning call is made; this is brief for an imminent danger, such as a fast-flying bird of prey, but is more prolonged for a slow-moving threat, such as a snake. Population size varies, with densities of over 50 individuals per hectare in favourable breeding seasons.
Brants's whistling rat does not exhibit any special physiological adaptations to reduce water loss in its arid environment, and obtains all its water needs from its plant foods. It is active in air temperatures between 23 and 37 °C (73 and 99 °F), and the burrow temperature is relatively stable despite wide swings in the outside temperature. It is most active in the early morning and the period approaching dusk, remaining underground during the hottest parts of the day. Where possible, foraging takes place from within the burrow, and the animal rarely ventures beyond 30 cm (12 in) of a burrow entrance. The diet consists of leaves, stems, grasses, succulents and bulbs, but not seeds or other dry materials.