Following Tenbun-honan (Tenbun Hokke War) in the Muromachi period, Honzen-ji Temple received rinji (the Emperor's command) from Emperor Gonara to became chokugan-ji (a temple built at the order of the emperor).
室町時代の天文法難後、後奈良天皇より綸旨（りんじ）を賜り、勅願寺となった。