The history of the University goes way back to the early years of missionary work in East Africa, with learning commencing in 1875, in Frere Town, near Mombasa.
The Church Missionary Society (CMS) founded a settlement for freed slaves at Frere Town, near Mombasa.
The Rev. E. A. Fitch began a Divinity class designed to offer some practical skills and Christian leadership training to the freed slaves. The Divinity class offered training to six teacher-evangelists who were ordained Deacons, and subsequently began training of Africans for the ordained ministry of the Christian Church.
The Rev. H. K. Binns laid the foundation stone of St. Paul's Divinity School at Frere Town, Mombasa, on the 28th July.
The foundation stone for the St. Paul's Divinity School was transferred to the main campus in Limuru in January.
The Presbyterian Church of East Africa and the Methodist Church in Kenya joined the Anglican Institution and brought in their ministerial candidates for training.
A transitional union was accomplished when the three Churches formed a College Council to run the affairs of the College.
The CMS St. Paul's Divinity School became St. Paul's United Theological College on 1st January.
The Reformed Church of East Africa formally joined the three other Churches as the fourth Participating Partner.
The National Council of Churches of Kenya in its corporate identity was admitted by the Governing Council as the fifth Participating Partner in the ownership of the College. The University is based upon the partnership of the four Participating Churches and the NCCK as a corporate body with the representation in the Governing Council being ACK 50%, PCEA 20%, MCK 10%, RCEA 10% and NCCK 10%.
The institution was awarded a Charter to become St. Paul's University on 14th September.