The shrine was relocated from its original site in present-day Ueno Park in 1625 to make way for Kan'ei-ji Temple, one of the Tokugawa shogunate's most important religious institutions.

The shrine's main deity, Ono no Takamura, was a legendary poet-scholar said to serve as a bureaucrat in hell at night while working for the emperor by day, traveling between realms through a well in Kyoto.

The shrine hosts a unique 45-minute non-stop bean-throwing ceremony during Setsubun, where children are organized by age into safety zones and adults receive treats from shrine maidens since the beans can't reach them.

The current shrine buildings survived both the 1923 Great Kanto Earthquake and the 1945 Tokyo firebombing, making the 1866 main hall a rare example of late-Edo period architecture still standing in Tokyo.