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 located a sake museum, various stores selling a variety of goods, and there are lots of stones in which are the names of donators to the shrine carved in kanji-characters. Due to the Honji suijaku theory which claimed the local kami were incarnations of Buddhist gods, Kotohira shrine was in times prior to 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), and in 1165 the spirit of Sutoku-Tennō was also enshrined.
Prior to 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.