The yellow-faced honeyeater was first described, and placed in the genus Sylvia, by ornithologist John Latham in his 1801 work Supplementum Indicis Ornithologici, sive Systematis Ornithologiae. French ornithologist Louis Jean Pierre Vieillot described it as Melithreptus gilvicapillus in 1817, and English zoologist George Robert Gray as Ptilotis trivirgata in 1869. The specific name chrysops is derived from the Ancient Greek words " Chrysos" meaning "gold" and " Prosopo" meaning "face", in reference to the stripe of yellow feathers.
The yellow-faced honeyeater was classified in the genera Meliphaga and then Lichenostomus until 2011. Delineating the latter genus had been systematically contentious, and evaluations of relationships among honeyeaters in the genus using dense taxon and nucleotide sampling confirmed previous findings that Lichenostomus is not monophyletic. Five species have previously been described as comprising the Caligavis subgroup, but studies using the mitochondrial DNA identified the yellow-faced honeyeater as most closely related to the black-throated honeyeater (C. subfrenatus) and the obscure honeyeater (C. obscurus) of New Guinea; they were therefore grouped into the genus Caligavis. The bridled honeyeater (B. frenatus) and the Eungella honeyeater (B. hindwoodi) were sufficiently different to be placed in a separate genus as Bolemoreus. A 2017 genetic study using both mitochondrial and nuclear DNA found the ancestor of the yellow-faced honeyeater diverged from the common ancestor of the other two Caligavis species around seven million years ago.
There are three subspecies, two described by Gregory Mathews in 1912. There are only very slight differences between the nominate race and C. c. samueli found in the Mount Lofty Ranges in South Australia and C. c. barroni from Clarke Range and the Atherton Tableland in Queensland. The latter race is described as "poorly differentiated" and "possibly not worthy of recognition" by the Handbook of the Birds of the World.
Surgeon-General to the First Fleet John White caught a specimen in May 1788, calling it a yellow-faced flycatcher in his Journal of a Voyage to New South Wales, which was published in 1790. Latham called it the black-cheeked warbler. John Gould called it the yellow-faced honeyeater in 1848, which has become its official name. It is also known as the yellow-gaped honeyeater, or the quitchup, in reference to its call.