Nishina Shrine was established by the Nishina Family who ruled the Shinano area from ancient times to the middle ages. The shrine was founded to pay respects and to be a 'mikuriya' shrine for the Grand Shrine of Ise. 'Mikuriya' means a building where food and drink are prepared specifically for the gods worshipped in the shrines.

The exact date of the shrine's completion is not clear but it is said to be around the 2nd year of the Kowa era, during the Heian period.

The main building is constructed using 'kiritsuma-zukuri' and straw-thatching, both typical of 'shinmei-zukuri' architecture. The building was reconstructed every 20 years, but when it became a place mainly used for prayer under the Matsumoto Domain in the Edo period, reconstruction was changed to renovation. The last complete reconstruction was made in 1636.

Nishina Shrine is the oldest 'shinmei-zukuri' style building in Japan, and is designated as a National Treasure. Furthermore, the wooden 'munefuda', dating to 1376, and the bronze Buddha, which are both kept in the shrine, are designated as Important Cultural Treasures.

Traditional events, including divine rites from ancient times for sowing rice, as well as Shinto dance and music performances during the Great Festival of Autumn, are still carried out at this shrine.