Pi Alpha Alpha shares offices and staff with the National Association of Schools of Public Affairs and Administration. NASPAA is a professional education association dedicated to the advancement of education, training, and research in public policy and administration. The Association's membership consists of the undergraduate and graduate education programs in public affairs and administration of more than 250 academic institutions in the United States. Affiliated with NASPAA are many federal, state, and local government agencies, university public affairs and administration programs in other nations, and national public interest groups all of whom share a concern for improving the quality of public management.

Collegiate programs in public affairs and administration are represented in NASPAA through the programs dean or director, called the program's "principal representative" to NASPAA. The principal representative may serve as the local Pi Alpha Alpha chapter faculty advisor or another member of the program's faculty may be designated to serve as the advisor. Communications between local chapters and the national office typically flow between the chapter advisor and the national staff.

The national organization of Pi Alpha Alpha is directed by a national president, vice-president, and national council comprised of twelve members elected to four year overlapping terms. The president and vice-president each serve two year terms; the vice-president also serves as president elect and succeeds to the office of president. Officers are elected at the society's biennial meeting, held in the fall of each odd numbered year in conjunction with the Annual Conference of NASPAA. In addition, a national director, appointed by and serving at the pleasure of the national council, provides the society with staff support.

Each local chapter is notified of the biennial meeting at least 90 days in advance and urged to send at least one delegate, who can be a student, alumni, faculty, or honorary member, to attend and vote in the session.