It was gazetted a townsite in 1856,[3] deriving its name from the nearby Wonnerup Inlet.

The meaning of the name is "place of the woman's digging or fighting stick"; the Noongar word for fighting stick is wonna, while the suffix -up denotes place of.

The wonna was made from the peppermint tree, Agonis flexuosa, a coastal native found only in the south-west, and was a common trade item of the Noongar people.

[4] The Wonnerup massacre of Wardandi Noongar people by European settlers occurred in the vicinity of the area in 1841.

In 1998, part of Wonnerup was subsumed into the Busselton suburb of Geographe.