Kunzea muelleri was first formally described in 1867 English botanist George Bentham in his publication Flora Australiensis from a specimen collected by Victorian Government Botanist Ferdinand von Mueller. Mueller collected plants from the Haidinger Range, Mount Wellington and the Munyang Mountains and had given the species the name Kunzea ericifolia in 1855. This name was later deemed illegitimate as it has been previously assigned to another species. The specific epithet (muelleri) honours Mueller.