Empress Tachibana-no-Kachiko (786-850), the consort of Emperor Saga (786-842), founded a big convent called Danrin-ji some time in Jowa era (834-848) in this place. In the middle of Heian period (794-1192) the convent fell into ruin. Retired emperor Go-saga (1220-1272) built a detached palace called Kameyama-dono on the deserted convent site. Kameyama-dono was inherited by Emperor Kameyama (1249-1305) and his grandson Emperor Go-daigo (1288-1339).

In the year 1339, Priest Muso Soseki made a proposal to the first Muromachi Shogun, ASHIKAGA Takauji (1305-1358) and his brother Tadayoshi (1306-1352) about establishing a temple for the late emperor Go-Daigo, who had initially coordinated with the samurai brothers to overthrow the Kamakura Shogunate and then changed to be the deadly enemy of them. They agreed with the priest but the newly-established Shogunate government did not have enough money so that they had to start trade with China to make funds for building the temple.

In the year 1345, the Zen temple was officially founded with Muso Soseki being the first head priest. The buildings of the temple suffered fires several times during its history. The present O-Hojo building was rebuilt in 1899 followed by other buildings.