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CUEA was founded on 3 September 1984 in Nairobi Kenya as a Graduate School of Theology, under the name the Catholic Higher Institute of Eastern Africa (CHIEA). The Institute was founded by the regional ecclesiastical authority known as Association of Member Episcopal Conferences of Eastern Africa (AMECEA). The member countries of AMECEA are: Eritrea, Ethiopia, Kenya, Malawi, Sudan, Tanzania, Uganda and Zambia.Initially, CHIEA offered two-year Licentiate/MA programmes in Theology, as authorized by the Congregation for Catholic Education, Vatican City (cf. Prot. N. 821/80/34), effective 2 May 1984. On 3 September of the same year, it was officially inaugurated by the Right Reverend Bishop Medardo 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 to establish 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. The Institute rebranded as the Catholic University of Eastern Africa, in 1992.

In 2002, the Faculties of Science and Commerce were established. Then in 2003, the Center for Social Justice & ethics was established. The Faculty of Law was established in 2004, and the School of continuing professional development in 2009. In 2009, satellite campuses were established in Eldoret and Kisumu.In April 2013, the university opened a new campus in the I&M Tower, along Kenyatta Avenue, in the Nairobi's central business district. The campus can accommodate up to 500 students.