The Church of Christ in Japan was founded by American missionaries in 1872. J.C. Presbyterians like Hepburn and S. R. Brown and the Reformed J. H. Ballagh were among the founders, in Yokohama. In 1877 the church unified with the Presbyterian Association. By the end of the 19th century membership was 10,500 and there were 72 congregations. In the following fifty years it was among Japan's largest churches. It sponsors missionaries in Korea, Hong Kong and Singapore. In 1941 the denomination become part of the United Church of Christ in Japan. In 1951, 39 congregations reconstructed themselves as the Church of Christ in Japan.
The church has 13,102 members and 137 congregations.