Christianity was established in Nigeria with the arrival in 1842 of a Wesleyan Methodist Church missionary. He had come in response to the request for missionaries by the ex-slaves who returned to Nigeria from Sierra Leone. From the mission stations established in Badagry and Abeokuta, the Methodist church spread to various parts of the country west of the River Niger and part of the north.

In 1893 missionaries of the Primitive Methodist Church arrived from Fernando Po, an island off the southern coast of Nigeria. From there the Methodist Church spread to other parts of the country, east of the River Niger and also to parts of the north. The church west of the River Niger and part of the north was known as the Western Nigeria District and east of the Niger and another part of the north as the Eastern Nigeria District. Both existed independently of each other until 1962 when they constituted the Conference of Methodist Church Nigeria. The conference is composed of seven districts.

The church has continued to spread into new areas and has established a department for outreach/evangelism and appointed a director of evangelism. An episcopal system adopted in 1976 was not fully accepted by all sections of the church until the two sides came together and resolved to end the disagreement. A new constitution was ratified in 1990. The system is still episcopal but the points which caused discontent were amended to be acceptable to both sides.

The Methodist Church Nigeria (MCN) has been at the forefront of spiritual and social transformation, by spreading spiritual holiness and investing in medical-health services and social-economic welfare of the people. The church has established various institutions like the leprosy centre, three mentally ill-destitute centres, and an orphanage centre, for children orphaned by HIV/AIDS. These centres reach out to the rejected and less privileged members of society. They also ensure reintegration of those previously treated as outcast and subjected to various societal abuses. In the area of health MCN has established the Wesley Guild Hospital and several Methodist hospitals spread over the country which provide good healthcare services in their environments. In addition to all other services MCN has from the beginning placed a very strong emphasis on the need for education.

Throughout the country, the Church has established numerous schools, from kindergarten through primary to senior secondary schools and theological institutions which have produced men and women who have contributed and are still contributing very significantly to all spheres of human endeavour.

The  prelate presides over the conference, the overall governing body of the church. This conference meets every two years to deliberate and take decisions on all issues affecting the life of the church. The conference area is divided into eight archdioceses. Each archdiocese is composed of not less than four dioceses over which an archbishop presides at the archdiocesan council meetings.  The constitution of the church provides for lay participation in the leadership of the church from the local church through to conference level.