Located at 521m halfway to the top of Mount Zōzu, the shrine stands at the end of a long path, with 785 steps to the main shrine and a total of 1,368 steps to the inner shrine. Since the Muromachi Period pilgrimages to the shrine became popular, and even today usually hundreds of visitors in a day climb the steps of Mount Zōzu. On the way to the shrine is a sake museum, stores, and stones with the names of donors carved in kanji. Due to the Honji suijaku theory which claimed the local kami were incarnations of Buddhist gods, Kotohira Shrine was in times before the Meiji era equally a Buddhist and a Shintoist sanctuary.
The principal kami of the shrine is Ō-mono-nushi-no-mikoto, a spirit associated with seafaring (also referred to as the Buddhist deity Konpira). In 1165 the spirit of Sutoku-Tennō was also enshrined.
Before the Meiji period it was known as Konpira-Daigongen(金比羅大権現?), and it stood at the head of the nationwide group of shrines bearing the names Kompira and Kotohira. The ema hall is the site of prayers for safe seafaring.