The Faculty of Medicine Council at the Arab American University is the highest academic body responsible for supervising the Faculty affairs and ensuring the efficient running of academic and administrative work. The Council is headed by the Dean of the Faculty and includes the Dean's Assistants and the heads and coordinators of the various academic departments. The Faculty of Medicine is subject to the same provisions as the rest of the University's faculties regarding the establishment of a faculty council, which are included in the following articles of the University Councils' Instructions.

 The Council has broad authorities, including proposing and amending study plans in cooperation with the department councils, and then submitting these plans to the Vice President for Academic Affairs for study and approval by the Deans' Councils. The Council also performs a vital role in recommending student admission requirements, supervising the organization of study in the faculty, and ensuring effective coordination between the various departments. In addition, the Council is responsible for organizing exams, supervising procedures, and publishing their results.

 The Faculty Council's tasks include recommending the awarding of academic degrees and certificates, in addition to supervising the organization and encouragement of scientific research in the Faculty. One of its important tasks is to make recommendations on issues related to faculty and administrative staff, including appointments, promotions, transfers, study leaves, and resignations, in line with University regulations and instructions. The Council also prepares the Faculty’s draft budget and forms various committees that contribute to the smooth workflow the Faculty.