The place name Ninnaji, where Ninnaji Shrine is located, comes from the fact that it was once the territory of Ninnaji Temple in Kyoto. The shrine is thought to have been founded in the early Muromachi period, and at that time it was called Hakusan Gongensha. In 1633 (Kan'ei 9), Nagai Shinano no Kami Naomasa became the lord of the domain, and began to worship Sugawara no Michizane, and since then it has also been called Tenmangu Shrine. It is said that the shrine building was washed away when the Yodo River levee broke, so it was moved to its current location in the center of the village. Many trees are planted within the shrine grounds.