As an interdenominational congregation, Tokyo Union Church maintains full fellowship with Christian bodies and fulfills its discipleship through cooperative efforts in Japan and around the world. It is a charter member of the National Christian Council of Japan
and the Tokyo Ecumenical Council. This church recognizes ecumenical relationships with other church bodies in Japan, other international union churches around the world, and the World Council of Churches
. It also recognizes a relationship with the Network of International Congregations
as a point of contact for consultations, association with other international union churches, and mutual assistance.