Eremophila pusilliflora was first formally described by Bevan Buirchell and Andrew Brown in 2016 and the description was published in Nuytsia. Prior to its formal description it was known as Eremophila sp. 'Princess Range'. The specific epithet (pusilliflora) is derived from the Latin words pusillus meaning "little" and flos meaning "flower", referring to the flowers of this species which are smaller than those of the similar "E. forrestii.
