Jinja Honcho took its present form on 2 February 1946, when three predecessor bodies, the Koten Kokyujo, an educational institute for Shinto priests, the Dainippon Jingikai, a prewar national Shinto association, and the Jingu Hosaikai, devoted to Ise Grand Shrine's worship, merged into a single nongovernmental association. The merger complied with the Allied occupation's Shinto Directive of December 1945, which had abolished the prewar Institute of Divinities, a Home Ministry branch that had administered State Shinto, and separated Shinto from government support or control. Jinja Honcho organized as a religious corporation, or shukyo hojin, under the legal framework the postwar Japanese government put in place for every religious body: the Religious Corporations Act, Law No. 126 of 1951, effective from April of that year, giving a religious organization juristic personality to own and administer its own property independent of the state.
Its internal governance runs through three named offices: a Sosai, a ceremonial head; a Tori, or vice-leader; and a Socho, the secretary-general who runs its day to day administration. Beneath them a graded system of five priest ranks, from the senior jokai down to the junior chokkai, orders the roughly 20,000 priests serving its member shrines, and Jinja Honcho trains and certifies the qualifications a shrine needs before it can hire one.
More than 79,000 of Japan's approximately 80,000 Shinto shrines belong to Jinja Honcho, by far the country's largest Shinto religious body. A number of prominent shrines, including Yasukuni Shrine, administer their own priesthood and calendar independently, remaining outside the structure the 1946 merger built for the rest of Shinto.