The major foundation of what has become Bowen University today was laid in 1854. That year, the family of the late Rev. Thomas Jefferson Bowen started a school in Ijaiye Orile in the present Oyo State of Nigeria. The School, comprising five stewards of the late Bowens, five other labourers, and a few others drawn to the fledgling school by sheer curiosity, has grown from this little beginning in 1854 into thousands of Baptist Primary and Secondary Schools scattered across the country. By 1960, there was a Baptist school almost everywhere there was found a Baptist congregation.

The idea of establishing a Baptist University in Nigeria was first conceived in 1938. This was borne out of the Baptist’s commitment to assist the people to develop their potential to the fullest. The first bold step towards actualising this vision was not taken until 1956 when a proposal was presented to the meeting of the Baptist Mission held in Eku from 11th to 14th December 1956. On 16th and 17th July 1957, the joint meeting of the Executive Committees of the Baptist Mission of Nigeria and the Nigerian Baptist Convention endorsed the idea. Since then, the Nigerian Baptist Convention has worked tirelessly, committing time, material and human resources to actualising the vision. Today, all these efforts have crystallised into the establishment of Bowen University, a significant landmark in the academic heritage of the Nigerian Baptist Convention, making it the first Baptist University in Africa.

On the 17th of July 2001, the Federal Government of Nigeria approved the establishment of Bowen University and was subsequently licensed to operate by the National Universities Commission (NUC).

On 4th November 2002, Bowen University commenced academic activities with 506 pioneering students admitted into its three faculties: Agriculture, Science and Science Education, and Social and Management Sciences.

In 2009, the National Universities Commission (NUC) approved the University to offer degree programmes in Medicine (MBBS), Anatomy (B.Sc) and Physiology (B.Sc). In June 2011, NUC also approved the University to establish the Faculty of Humanities and Faculty of Law. The Faculty of Humanities began immediately in 2012, while the Council of Legal Education sent its Panel of Facility Visitation in August 2012 and gave approval in December of the same year. These programmes have commenced in earnest.