The foundation of Mikami Jinja is uncertain. While it is known that Fujiwara no Fuhito ordered the construction of a shrine at the current location in 718 AD, archaeological excavations have found that the area was connected with rituals pertaining to Mount Mikami from a much earlier period. In the Meiji period, 24 dōtaku were excavated at the foot of the mountain, indicating that it was worshipped from the Yayoi period.
The shrine is mentioned in several occasions in the Nihon Sandai Jitsuroku completed in 901 and is also mentioned in the Engishiki list of shrines in Ōmi Province dated 927 AD.
The shrine's main building is estimated to have been built in the latter half of the Kamakura Period from its various stylistic details. If fuses Shinto shrine architecture with Buddhist elements such as Irimoya-zukuri, style roof, plaster walls, and "Renko" windows. It was declared a protected building as early as 1899, but was formally designated as a National Treasure in 1952.[2]