Rinnoji Temple is a generic name of 15 subordinate temples. History of Rinnoji Temple goes back to 766. Priest Shoto built Shihonryuji Temple near Shinkyo Sacred Bridge in that year. Nikko became popular place for mountainous worship and many ascetics visited there. Imperial court gave a name of Manganji Temple in 810. Also, Saint Ennin introduced Tendai sect in Nikko later. In Kamakura period, Benkaku established Koumyouin House and designated it as a main house of Nikko. Also, successor was invited from the Imperial family. That became a tradition. However, territory of Nikko was confiscated by Hideyoshi Toyotomi in the warring states period because Nikko was on the opposite side of Hideyoshi. Popularity of Nikko declined temporary.

Bishop Tenkai revived Nikko in 1613 when he became a leader of Tendai sect in Nikko. He built Toshogu Shrine, and Nikko became more popular than ever before. In 1655, the successor Shuchouhoushinno renamed himself as Rinnoji-no-miya. The name of Rinnoji Temple was derived from the former successor.

Rinnoji Temple was driven into the corner in Meiji period. Meiji government announced the law, which separates Buddhist temple and Shinto shrine. However, there was no border between Buddhistm and Shintoism. Also, successor term of Rinnoji was abolished in 1869, and Rinnoji was named Manganji again. More than 109 temples were merged to Manganji Temple by the law.

However, 15 temples of Nikko overcame the hardship and revived in 1882. Rinnoji Temple and its successor term were revived in the next year. Visitors will not be able to see all of historical aspects of Rinnoji Temple in a day because there are so many.