It was originally intended that Emperor Godaigo's son Imperial Prince Yoyoshi originally would found the temple and invite Genno Hongen to serve as the first head priest of Rinsen-ji Temple but he died before the construction of the temple was completed, so his father acted as founder and appointed Muso Soseki as the first head priest in 1335.
この寺は、当初後醍醐天皇の皇子世良親王が元翁本元を開山として招いて創建しようとしたが、親王が建立する前に没したことから、父の後醍醐天皇が1335年（建武(日本)2年）夢窓疎石を開山として建立したものである。