In accordance with the International Code of Zoological Nomenclature, the name Apomys gracilirostris is a binomen. The generic name, Apomys was proposed by American biologist Edgar Mearns in 1905 and has the meaning of mouse from Mount Apo (mys, μῦς, being the Ancient Greek word for mouse); this because the type species of the genus was first found on Mount Apo. The specific name, gracilirostris, is a combination of the Latin words gracilis slender and rostrum snout and refers to the animal's long, slender snout.