The Wakayama Prefectural Museum has its origins as the Prefectural Museum of Art, which was established in 1963. It was established in 1971 as a public museum on the site of the Ninomaru ruins of Wakayama Castle, and in 1994, it was relocated and opened along with the Prefectural Museum of Modern Art to a new site on the site of the former Faculty of Education of Wakayama University on the south side of Wakayama Castle.