The highest decision-making body of the Mustafa Center is the General Body which consists of members of the Center who pay a membership fee or are otherwise approved as members due to their extraordinary services to the Center or the community.

The General Body elects five members of the 9 member Board of Directors for a period of two years. The Imam and three members from the Afghan Academy, who have automatic membership, constitute the remaining four members of the Board.

The Board of Directors, in turn, chooses one of its members as the President of the Executive Council.

The President of the Executive Council nominates his/her Vice Presidents and Committee Chairs with the approval of the Board of Directors.

The Board oversees the affairs of the Center whereas the Executive Council runs its day-to-day affairs.