The history of Zuishin-in begins with the monk Ningai, an eighth-generation disciple of the renowned Kōbō Daishi, founder of Shingon Buddhism. In the year of 991, Ningai built Zuishin-in as a sub-temple of Gyuhizan Mandara-ji and as a place for monks to live.

Monk Ningai was also known as “The Rain Monk.”

Kōbō Daishi, the founder of Shingon or "mantra" school of Buddhism, was the first to summon the power of the dragon gods for rain at Shinsen-en Garden. Since then, the Shingon monks were ordered by the court to follow the same ritual, especially in years of drought. Monk Ningai was able to make it rain nine times. With respect and admiration, he was named “The Rain Monk.”

Ono no Komachi appears in another tale, this time about praying for rain.

It was a year of drought, when no matter how many priests would pray for rain, not so much as a cloud would appear. Desperate for salvation, the emperor ordered Ono no Komachi to try to appease the gods with her poetry.

Even the almighty gods of old never knew such beauty
as to the opening of the Milky Way.

"God, have you seen the drought? Then show Your power and open the gates of the Milky Way."

As soon as she finished her poem, the sky was covered with dark clouds and it was raining like the sky had split wide open. This poem is recorded in the collection of Komachi poems called "Komachi-shu," but is said to be written by someone after her death.