Nagono Jinja stands adjacent to Nagoya-jo, the castle where Nobunaga's father Nobuhide resided, and which Nobunaga himself held for a time. As the guardian of 'Nagono' — the origin of the name 'Nagoya' — this shrine held particular significance for Nobunaga as he consolidated control over Owari.

In 1610, when Ieyasu built Nagoya Castle, this shrine lay on ground that would fall within the castle precincts. Ieyasu drew a sacred lot to ask the deity's will, and the answer forbade relocating the shrine, so it was left in place — coming to stand in the Sannomaru district facing the main gate of the Ninomaru. Thereafter it was cherished under the Owari domain as the guardian shrine of Nagoya Castle and the tutelary deity of the city.