This species was first formally described in 1871 by Charles Moore and Ferdinand von Mueller who gave it the name Euodia polybotrya. The description was published in Fragmenta phytographiae Australiae from specimens collected on Mount Lidgbird. In 2001, Thomas Gordon Hartley changed the name to Melicope polybotrya in the journal Allertonia. The specific epithet comes from the Greek polys (many) and botrys (bunch), referring to the clusters of flowers in the type specimen.