The kami enshrined at Yahiko Jinja is: The foundation date of Yahiko Shrine is unknown, but the shrine dates to prehistoric times as it is referred to as "ancient" in a poem even in the Nara period Man'yōshū.

Per the shrine's legend, Ame-no-Kaguyama-no-mikoto landed from the heavens at Nozumihama (in what is now the city of Nagaoka) and taught local people about industries such as fishing, salt production, rice cultivation, and sericulture.

The subsequent history of the shrine is uncertain and often contradictory, as most old records have been lost in fires and other disasters over the years.

The shrine was well patronised by the military samurai class, and the shrine treasury has a Muromachi period Ōdachi Japanese sword which is an Important Cultural Property of Japan as well as amor and swords donated by Minamoto no Yoriie, Minamoto no Yoshitsune and Uesugi Kenshin.

[7] During the Edo period, the daimyō of Takada Domain, Matsudaira Tadateru granted the shrine estates with a kokudaka of 500 koku for its upkeep/ During the Edo Period, the kokugaku scholar Hirata Atsutane claimed that the shrine had preserved in Jindai moji, predating the introduction of Chinese-based kanji, but that these records had been lost in a fire.