Sheppard and Lapsley Presbyterian University of Congo is governed by the Presbyterian Committee on Ministries (CPM), an 11-member board called comprised of the Rector of the university, five members from the Presbyterian Community of Congo (CPK), and five members from the Presbyterian Community of Kinshasa (CPK). The President of the CPM is Rev. Tshimungu Mayela of the CPK. The Rector is the Rev. Dr. Mulumba Musumbu Mukundi.
Normally this governing board meets once a year to receive reports and correspondences, and to discuss them as appropriate in the three commissions: program and scholarships; planning and nominations; and finances. Through recommendations from these commissions, the board nominates personnel to the various administration and teaching positions, determines the annual budget, plans major developments, and decides on miscellaneous issues brought to its attention.