Founded by the monk Ennin (Jikaku Daishi) by imperial wish of Emperor Saga in the 834–847 period.

Founded as a Tendai temple by Ennin, it later became connected to Honen, and his mausoleum was built in its grounds. It preserves the footsteps of Honen, who spread the nembutsu.

Within Nisonin's precincts stands a stone marker traditionally identifying the site of the 'Shigure-tei' (Passing Shower Hermitage), the mountain retreat of the great Kamakura-period poet-scholar Fujiwara no Teika (1162–1241). Around 1220 and into his later years, Teika is said to have stayed frequently at this retreat on Mt. Ogura, composing and studying poetry while overlooking the beautiful Sagano landscape. It was here, at his Ogura Mountain hermitage, that Teika is believed to have compiled the hundred poems later known as the 'Ogura Hyakunin Isshu' (One Hundred Poems by One Hundred Poets), which became one of the most celebrated anthologies in the history of Japanese poetry.