Pi Alpha Alpha is affiliated with NASPAA, the international association of 280 schools of public policy, public affairs, and public administration.  Only schools that are members of NASPAA can host a Pi Alpha Alpha chapter. Chapter advisors must be faculty members in the NASPAA member program.

Pi Alpha Alpha is directed by a national president, vice-president, and national council comprised of 12 members elected to four-year terms. The president and vice-president each serve two years; the vice-president also serves as president-elect. Officers are elected at the society's biennial meeting, held in conjunction with the NASPAA Annual Conference. 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.