The Association is structured as a democratic organization with decision-making vested in a House of Delegates, a Board of Directors and the Office of the Executive Vice President.

The House of Delegates meets annually and is responsible for the adoption of educational policies for the Association. The House also approves new institutional members, establishes dues, approves the Association’s strategic plan and amends the AACP Bylaws as needed. All U.S. schools of pharmacy are regular or associate members of AACP. Each regular member has two votes in the House, one vote representing faculty and the other representing administration. On even numbered years the delegates elect the Speaker of the House. 

The Board of Directors consists of three presidential officers, the speaker of the house, the treasurer, three representatives of school administrations, three representatives of school faculties, three representatives of the AACP sections and the executive vice president. The Board generally meets three times a year to authorize policy and program implementation, and to consider significant matters related to the operational and financial affairs of the Association.

The executive vice president is selected and employed by the Board of Directors as the chief executive officer of the Association, with overall responsibility for the administration of the policies and programs adopted by the House of Delegates and the Board of Directors. The Association's staff is appointed by the executive vice president, who is responsible for all actions taken by staff members on the Association's behalf.