Two missionary doctors of the Church Missionary Society evangelized the eastern region of Rwanda in 1914-16. The first station of the Rwanda mission was established in 1925. The work grew with the revivals in the 1930s and 1940s. The first Rwandan bishop was appointed in 1965. That same year the church was called the Eglise Anglicane du Rwanda and was part of the Province of Rwanda, Burundi and Boga-Zaïre. In 1992 the church became an autonomous province within the Anglican Communion.

Like all strata of Rwandan society, the church suffered through the genocide, and one of its major priorities is to replace clergy through training. The church has a role as a healing ministry to the many traumatized people in Rwanda and in reconciliation, restoration, and rehabilitation. The church has also been involved in rural development, medical work, vocational training, education, and in the struggle against HIV/AIDS.