The hoopoe was classified in the clade Coraciiformes, which also includes kingfishers, bee-eaters, and rollers. A close relationship between the hoopoe and the wood hoopoes is also supported by the shared and unique nature of their stapes. In the Sibley-Ahlquist taxonomy, the hoopoe is separated from the Coraciiformes as a separate order, the Upupiformes. Some authorities place the wood hoopoes in the Upupiformes as well. Now the consensus is that both hoopoe and the wood hoopoes belong with the hornbills in the Bucerotiformes.
The fossil record of the hoopoes is very incomplete, with the earliest fossil coming from the Quaternary. The fossil record of their relatives is older, with fossil wood hoopoes dating back to the Miocene and those of an extinct related family, the Messelirrisoridae, dating from the Eocene.