It was opened in Alice, Transkei in 1963, in response to apartheid legislation such as the Group Areas Act which forced theological colleges for black students that were situated in "whiter" areas to close or move.
The denominations affected by this got together and decided to build a new joint seminary on land next to Fort Hare University College at Alice in the Transkei.
They opted for the model of English collegiate universities, like Oxford, Cambridge and Durham, where each college functioned independently, but shared resources such as teaching staff and libraries.
On 26 November 1974, the government issued an expropriation order, giving the Seminary three months to vacate the land and the buildings.
The seminary was obliged to move, first to Umtata in Transkei, then in Edendale and finally a new campus was opened in August 1980 at Imbali, Pietermaritzburg.