In addition to the ruins dating back to the Jōmon period, the Tsuno area is home to more than 20 burial mounds (the Tsuno Kofun Cluster), and pottery and stone tools have been excavated near the site of the shrine.

By the Muromachi period the Tsuno Shrine was regarded as the ichinomiya of Hyūga Province.

The shrine was restored in its current form by Akizuki Tanemasa, the daimyō of Takanabe Domain, and in 1701, estates worth 20 koku were donated for its upkeep.

Successive daimyō of Takanabe supported the shrine through the end of the Edo period.

[4] in 1934, the area of the shrine was expanded and improved as part of the "celebrations of the 2600th anniversary of the founding of Japan" project sponsored by the government.