The shrine has many structures from the Muromachi period or older which are designated either National Treasures (NT) or Important Cultural Properties (ICP).

Per the shrine's own legend, it was founded during the time of the semi-legendary Emperor Suinin (who reigned 29 BC to 70 AD per the traditional calendar).

In 969 AD, it was recorded that the kami of Mount Kinpu from Yamato Province, Kunisatsuchi-no-mikoto [ja] was enshrined in a new main shrine building at the Namura Jinja.

During the Tenshō era (1573–1593), Oda Nobunaga presented the shrine with a saddle and a sword.

Namura Jinja is a 15-minute drive from Ōmi-Hachiman Station on then JR West Biwako Line.