Prostanthera schultzii was first formally described in 1896 by Ralph Tate from an unpublished description by Ferdinand von Mueller and the description was published in Report on the work of the Horn Scientific Expedition to Central Australia. The type specimens were collected on the higher slopes of Mount Sonder. In 1976, John Carrick changed the name to Wrixonia schultzii but in 2012 Trevor Wilson, Murray Henwood and Barry Conn changed the name back to P. schultzii.