Eucalyptus niphophila was first formally described in 1929 by Joseph Maiden and William Blakely in Maiden's book A Critical Revision of the Genus Eucalyptus, from material collected near Pretty Point on Mount Kosciuszko. In 1973, Lawrie Johnson and Donald Blaxell reduced the species to a subspecies of E. pauciflora as E. pauciflora subsp. niphophila. The epithet (niphophila) is derived from ancient Greek meaning snow-loving, referring to the alpine habitat of this eucalypt.