Hanazono Shrine was originally founded before the start of the Edo period, about 250 meters south of its present-day location. In the Kan'ei era, the shrine was relocated to the gardens of the Owari-Tokugawa family, in an area that had until then been a prolific flower garden, to make space for the villa of a shogun’s vassal. Before the Meiji period, a branch temple of a Shingon Buddhism sect was enshrined with Hanazono’s Shinto shrine, and the Buddhist chief priest served as the manager of both. During the Meiji Restoration that began in March of 1868, the Buddhist object of worship was abolished from Hanazono, and the religious space returned to only a Shinto shrine. At the time, it was named simply “town Inari shrine” because of a mistake in the submission to the official list of names. It was officially named "Hanazono Shrine" in 1965.