NIMS-GHANA is run by the Executive Board, made up of the NIMS Management Board (which includes representatives from all member Universities), the Executive Director and the NIMS directorate, who report to the NIMS Council. The NIMS Council is made up of All Vice Chancelors of all Member Universities, Representatives from GETFUND, Ministry of Education, Government, 2 representatives from Commitee of Vice Chancelors Ghana including its chairman,The Trust/Trustees and The Advisory Board.

The NIMS Council is set up to meet once a year in order to discuss and review academic progress and to consider the financial statements and the projected budget. The Advisory board advises on all academic aspects of NIMS programmes while initiating cutting edge programmes and projects that integrate Mathematics with industry, commerce and the Development of Ghana and beyond. The board also Initiates research projects for graduate and staff development in the Ghanaian framework. The trustee is cheritable trust and its board include the Committee of Vice Chancelor Ghana, The Executive Director of NIMS-GHANA and some appointed members. The management board is chaired by the Director of NIMS. The team must meet regularly to facilitate the relationship between NIMS and the other Universities.Members would assist in the selection of students for the Postgraduate Programme each year.

The NIMS Directorate is made up the Execurive Director, the unit Directors, various Coodinators and supporting staffs. There are currenly three unit directors made up of  the director of scientific and technical computing, the director of Programs and the Chairman of editorial Board. The Finance Coordinator, The Facility Coordinator, The Logistics coordinator, The Help and support Coordinator and The External Activities Coordinator constitute the unit coordinators of the institute. Other supporting staff includes the Administrative Assistant, Webmaster and the Videographer.