From the medieval to modern period, Joruri-ji Temple was a branch temple of Kofuku-ji Ichijo-in Temple but it transferred to the Shingon Ritsu Sect and became a branch temple of Nara Saidai-ji Temple (Nara City) during the turmoil of the anti-Buddhist movement at the beginning of the Meiji era.
中世から近世にかけて浄瑠璃寺は興福寺一乗院の末寺であったが、明治初期、廃仏毀釈の混乱期に真言律宗に転じ、奈良・西大寺(奈良市)の末寺となった。