Within the context of the current debate on the institutional transformation of the African Union (AU), this article examines the position of the chairperson of the AU Commission (Commission). The importance of the Commission chairperson cannot be over-emphasized. As the head of the “engine room” of the AU, it is pertinent that s/he is given the requisite powers to oversee the proper functioning of the secretariat, which would in turn propel the progressive development of African integration. This article argues that the current intergovernmental nature of the AU, where real decision making powers are held by member states, curtails the Commission chairperson from playing a meaningful role in the integration process. It highlights certain fundamental factors for ensuring the relevance of the chairperson. These include the institutional transformation of the AU, a review of the eligibility requirements for the Commission chairperson, a broad-based election process and hybridized functions.