The Catholic University of Eastern Africa (CUEA), like most other universities, started in a modest way. It commenced as a graduate school of theology known as the Catholic Higher Institute of Eastern Africa (CHIEA). The Institute (CHIEA) was founded in 1984 by the regional ecclesiastical authority known as the Association of Member Episcopal Conferences of Eastern Africa (AMECEA). Eritrea, Ethiopia, Kenya, Malawi, Sudan, Tanzania, Uganda, and Zambia are the member countries of AMECEA.
On 2 May 1984, CHIEA was authorized by the Congregation for Catholic Education, Vatican City (cf. Prot. N. 821/80/34), to offer two-year Licentiate/MA programs in Theology. On 3 September of the same year, it was officially inaugurated by Rt Rev. Bishop Madaldo Mazombwe, the then Chairman of AMECEA. On 18 August 1985, it was formally opened by Pope John Paul II. In 1986, the Graduate School of Theology started negotiations with the Commission for Higher Education in Kenya towards the establishment of the Catholic University of Eastern Africa (CUEA). In 1989, the Institute obtained the “Letter of Interim Authority” as the first step towards its establishment as a private university. After three years of intensive negotiations between the Authority of the Graduate School of Theology (CHIEA) and the Commission for Higher Education, the Faculty of Arts and Social Sciences was established. The climax of the negotiations was a granting of the Civil Charter to CHIEA on 3 November 1992. This marked the birth of the university as a private institution.
In 2002, the Faculties of Science and Commerce were established. Then in 2003, the Center for Social Justice & ethics was established.