It opened at Kilnerton in 1994, and was replaced by the Seth Mokitimi Methodist Seminary, located in Pietermaritzburg, KwaZulu-Natal, in January 2009, There is also a John Wesley College in Fiji, South Pacific.
The facility was first established as Kilnerton Institution in 1886 and situated in Weavind Park, a suburb of Tshwane (Pretoria), and was named after the Rev John Kilner, secretary of the Wesleyan Methodist Missionary Society who encouraged the formation of an indigenous clergy in South Africa.
There was also a request from local chiefs for the Methodist Church to provide land where they could safely settle.
Kilnerton became the site of the revival of John Wesley College when the Federal Theological Seminary of Southern Africa closed, opening its doors on 6 February 1994.
With the closure of the Department of Theology and Religion at Rhodes University in 2000, John Wesley College Kilnerton became the only centre for residential theological education in the Methodist Church of Southern Africa.