"Eucalyptus megasepala" was first formally described in 2006 by Anthony Bean and the description was published in the journal "Austrobaileya" from a specimen collected near Jowalbinna (near Laura).According to Bean, the specific epithet ("megasepala") is derived from the Greek "mega" (large) and "sepalum" (sepal), referring to the size of the sepals of this species compared to those of the related "E. tetrodonta".