The origin of the University goes back to the early years of missionary work in East Africa. In 1875 the Church Missionary Society (CMS) founded a settlement for freed slaves at Frere Town, near Mombasa. In 1888, the Rev. E.A. Fitch began a Divinity class designed to offer some practical skills and Christian leadership training to these freed slaves. The Divinity class offered training to six teacher-evangelists who were ordained deacons. Thus began the training of Africans for the ordained ministry of the Christian Church.
On the 28th July 1903, the Rev. H.K. Binns laid the foundation stone of St. Paul's Divinity School at Frere Town, Mombasa. This stone can be seen on the front of the present Chapel at Limuru to where the original Divinity school was transferred in January 1930.
The Divinity School continued as an Anglican Institution until 1949 when the Presbyterian Church of East Africa and the Methodist Church in Kenya joined and brought in their ministerial candidates for training. In 1954 the transitional union was accomplished when the three Churches formed a College Council to run the affairs of the College; and on the 1st January 1955, the CMS St. Paul's Divinity School became St. Paul's United Theological College. In 1973 the Reformed Church of East Africa formally joined the other three Churches as the fourth Participating Partner.
On the 18th of March 1993, 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. On September 14, 2007, the University was awarded a Charter to become St. Paul's University. 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%.