The Federation's membership comprises the medical boards of the United States, the District of Columbia, Puerto Rico, Guam, the Virgin Islands, the Commonwealth of the Northern Mariana Islands and 14 state boards of osteopathic medicine. Members of these boards are fellows of the Federation and many of them have been prominent in the affairs of numerous other major medical organizations. The Canadian provincial medical licensing authorities hold affiliate membership in the Federation. Individuals, physicians and non-physicians who are interested in licensing issues may become courtesy members through application to the Federation.

The Federation maintains valuable and constructive relationships with a variety of professional, licensing, and certifying organizations, including the American Medical Association (AMA), the Association of American Medical Colleges (AAMC), the American Osteopathic Association (AOA), other national medical groups, national organizations of licensing and certifying agencies in health-related fields and medical licensing authorities in several foreign countries. The Federation is a parent organization of the Accreditation Council for Continuing Medical Education (ACCME) and the Educational Commission for Foreign Medical Graduates (ECFMG), and member organization of the National Board of Medical Examiners (NBME). It was a founding member of what was to become the American Board of Medical Specialties (ABMS) and remains an associate member of that body. Additionally, a Federation representative sits on the board of the National Commission on Certification of Physician Assistants (NCCPA); a Federation board member also serves as the Federation's liaison with the Accreditation Council for Graduate Medical Education (ACGME).