The Yakata Shrine was constructed on top of the Doubutsu River terrace in 1572. During that time the shrine was on the grounds of the Doubutsu Castle. The castle was a specific type of castle called yakata in Japanese from which the Yakata Shrine gets its name. The castle was ruled over by Akamatsu Yoshitoki, who was an ally to Nobunao Nanbu. During the Kunohe Rebellion of 1591, the castle was destroyed by Kunohe forces.

Today, the gentle, sloping, cedar-lined path that leads from the torii gates to the shrine well preserves the original shape, construction, and unique characteristics that typify the style of Medieval Japanese castle architecture that was used in this area at the time the castle was built. Because of how well the site has preserved these characteristics it is considered a precious cultural asset. Additionally, within the shrine’s grounds is Aomori prefecture’s biggest Japanese fir tree. The tree’s trunk circumference is around 20 ft,  and the Japanese fir stands guard over the shrine in a silent but stately grandeur.