Isonokami shrine was highly regarded in the ancient era, and frequented by many members of the Imperial Family.

Early records show that the shrine was an emerging center of Yamato power, flavored with a military overtone.

Archeological evidences shows that around the 4th century, Yamato kings and nobility constructed more and more palaces and buildings in the shrine's vicinity.

[2] Prior to this, the Yamato leaders identified with kami worshipped at Mount Miwa, but may have turned to Isonokami for its martial implications.

Myths written in the Nihon Shoki clearly attempt to link the Yamato court to Isonokami shrine.

According to the Nihon Shoki, Emperor Suinin's eldest son, Prince Inishiki [ja] ordered a thousand swords made and was placed in charge of Isonokami's treasures.

[4] In 965, Emperor Murakami ordered that Imperial messengers be sent to report important events to the guardian kami of Japan.

A waka poem from the Man'yōshū anthology mentions Isonokami shrine, surrounded by holy cedar trees.