In accordance with the tradition of the university system in Nigeria, the Proprietor of Bowen University (i.e. the Nigerian Baptist Convention or NBC) runs the University through a Governing Council, as the highest policy-making organ of the University.
Members of the Governing Council are appointed by the NBC and they are men and women of Godly character first and foremost; erudite scholars and well-seasoned in their respective callings.
The Council is responsible to the Visitor to the University, who is the President of the Nigerian Baptist Convention.

The Governing Council is charged with the general control and superintendence of the policy, finances and properties of the University, as well as its public relations. The Governing Council has discharged these responsibilities with great dedication in spite of paucity of funds to run the University.
The Council carries out its functions through the following committees and organs:
Finance & General Purposes Committee
The functions of the F&GPC shall be the scrutiny of the University’s budget and other financial transactions before they are presented to Council.

The main function of the UAC shall be to undertake fund-raising activities for the University.

TENDERS BOARD

The main function of the Tenders Board shall be the consideration of tenders submitted by contractors wishing to execute projects for the University.

APPOINTMENTS AND PROMOTIONS COMMITTEE (A&PC)

The A&PC shall deal with the issues of the interview and appointment of staff of the University and present these to the Governing Council for its consideration. The A&PC will also consider staff of the University for Confirmation and Regularization of appointments and Promotion.

THOMAS JEFFERSON BOWEN FOUNDATION BOARD

The Board is to be based in the United States of America. It was set up by Council to raise funds abroad for the University, but is yet to be inaugurated.

DEVELOPMENT COMMITTEE

The Committee meets when it has matters to consider. The Committee met last about two years ago.

CONGREGATION

This is the forum where all degree holders in the University meet, at least, once in a semester to deliberate on the general state of affairs and the well-being of members of staff of the University.

CONVOCATION

Convocation meets every first Saturday of November to award degrees and honorary degree.

MANAGEMENT

The Committee sees to the day-to-day implementation of the Governing Council decisions and policies.

OTHER COMMITTEES

Other committees may be established as the Council may deem fit.