The organization of the Marien Ngouabi University is governed by the 2012 statute and 2013 decree reorganizing the UMNG. The organization has four administrative levels: the deliberative organs, the Rectorate, and the consultative and advisory bodies.

UMNG is headed by the Rector who is selected from among the permanent faculty of the rank of professor. Since 2010 this position has been held by Professor Armand Moyikoua. The Rector is assisted by two Vice-Rectors and a Secretary-General. One Vice-Rector is in charge of academic affairs while another is responsible for research and international cooperation. The Secretary-General is responsible for assisting the Rector in the administrative and financial management of the university.