There is little documentary evidence and it is uncertain when this shrine was first built. Architecturally, the buildings are constructed in the {{nihongo|Ōtori-zukuri|大鳥造||} which is believed to be a very ancient style of Shinto architecture, second only to the style of Izumo Taisha.  The first mention of the shrine in documentation comes from an entry in the Nihon Kōki dated 823 AD, in which the Imperial Court requested that the shrine pray for rain. The name also appears in the Shoku Nihon Kōki and the Nihon Sandai Jitsuroku, either in connection with prayer srelating to weather, or promotions in the shrine's official status. By the time of the 923 AD Engishiki, the shrine is styled as the only shrine in Izumi Province to be a {{nihongo| Myōjin-taisha|名神大社||}  and as an indication of its importance, an imperial messenger was dispatched to attend its annual Niiname-no-Matsuri. During this period, the shrine was under the control of , a Buddhist temple said to have been founded by Gyōki in either 708 AD or 740 AD. The temple had close connections with the Five regent houses of the Fujiwara clan. During the Kamakura period, branches of the shrine were built at many locations around the country, mostly in connection with shōen estates controlled by the Fujiwara, and around this time the shrine came to be called the ichinomiya of Izumi Province. During the premodern period, the main kami worshipped at the Ōtori-daimyōjin was Amaterasu, although the shrine's connection with the Yamato Takeru myth was well-known, and Yamato Takeru was enshrined as a secondary kami.