The Korean Christian Church in Japan traces its history back to 1908, when Korean students in the Tokyo area began worshipping together. The ecumenical character of the organization today reflects its early history.

Over 90 percent of the present Korean minority in Japan consists of Japanese-born Koreans and their children. As a minority church, the The Korean Christian Church in Japan has been involved in human-rights activities with a primary focus on the situation of Koreans in Japan. Its commitment to human rights and social issues began in 1968. In recent times, together with other Christian denominations and bodies, The Korean Christian Church in Japan has been actively involved in the movement for enacting the proposed legislation entitled “Basic Law for Foreign Residents”, which aims at preserving the human rights of foreign residents in Japan.

Since the 1990s the church has been developing its relationship with the Korean Christian Federation in North Korea, and has been working towards the reunification of the Korean peninsula. In July of 2002 The Korean Christian Church in Japan held its 8th Peace and Reunification Conference, inviting Christian leaders from North and South Korea.