MANEB is headed by an Executive Director. The Executive Director is assisted by a Deputy Executive Director who co-ordinates six departments; each headed by a director.
- Examinations Department— responsible for the development and conduct of all examinations.
- Computer Services Department— mainly concerned with data processing and analysis.
- Research and Test Development Department— responsible for research into quality of examinations and students' performance; development of test items, aptitude tests and training of assistant examiners among its responsibilities.
- Security Department— mainly responsible for provision of security to the development, processing, packing of examinations and administration of examinations It is further responsible for investigating examinations malpractices, development and installation of security measures and certification of candidates. Overall, it is responsible for the security of the MANEB's property and premises.
- Finance Department— responsible for financial management and its accounting.
- Administration Department— a service department, dealing with human resource management and general administration.