The species was named by Oldfield Thomas after John Ernest Buttery Hotson who collected the original 4 specimens in Balochistan in 1918.

Although they preferred the use of a local name, they reported that the languages of southern Pakistan do not distinguish among small rodent species (see haraam).

Instead, Norris et al. (2008) proposed that the species be referred to as Hotson's brush-tailed mouse, identifying a major morphological feature of the genus.

Because it was only known from the 4 specimens of the type series at the time, Baillie (1996) categorized Hotson's brush-tailed mouse as endangered.

The two species in Pakistan are distinguishable by several cranial characteristics and genetic evidence suggests they diverged roughly 2 million years ago (Norris et al., 2008).