The name is Aboriginal, and has been shown on maps of the region since 1839. 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.
Wonnerup was on the Bunbury to Busselton railway line, it was the point where the Nannup Branch Railway started on its route to Nannup after 1909. Before that it was part of the earlier 1879 railway and the 1898-1903 W.A. Timber Company railway line.