The churches which form the Association of Baptist Churches in Rwanda came into being through the work of a pastor from the Baptist Church in Congo and missionaries of the Conservative Baptist Foreign Mission Society. They came to Rwanda escaping the war of 1964 in then Zaïre (now DRC). They began the work of God in the northern part of Rwanda (Gisenyi and Ruhengeri) in 1966. Official registration took place in 1967. The churches which belong to the ABCR believe in: the holy scriptures, both Old and New Testaments; the Holy Trinity, God the Father, God the Son and God the Spirit; the nature of the human being created in the image of God without sin, and the fall after disobeying the divine law, becoming a sinner in the eyes of God; salvation found only in Jesus Christ. Those who repent and accept Jesus Christ as their Lord and Saviour are forgiven and saved. Those who are born again will inherit eternal life. Those who do not receive Jesus as their Lord and Saviour will be condemned to the eternal destruction. Since its creation, the ABCR has been very active in evangelization to fulfill the great commission given by the Lord Jesus Christ to his church. The Association has a Bible institute, a theological seminary and a theological university.

Apart from evangelism, the AEBR is also involved in other activities like education and health care. It has 20 secondary schools, 42 primary schools, two vocational training centres and three health centres. It is also active in community-based projects whereby local communities are grouped into small associations for income-generating activities. This is where the different needs of the people are addressed and come together to look themselves for adequate solutions.