The Physician Assistant Education Association (PAEA) was founded as the Association of Physician Assistant Programs in 1972 by a group of PA program faculty who saw a need to address the important issues of physician assistant (PA) programs’ accreditation; certification, continuing educational requirements, and role delineation for PAs; and the overall goal of improving the quality and accessibility of health care through the selection, education, and deployment of PAs.

For most of the first 34 years of its existence, the Association was housed in the same building as the American Academy of Physician Assistants and received management services from the Academy. In 2004 the Association's board made the decision to move the organization to fully independent status and employ its own staff. In October 2005, the Association's members voted to change the organization's name to the Physician Assistant Education Association and in May 2006 the Association moved into new office space as an independent organization.

The Association's membership grew rapidly in the 1990s as the number of PA programs nationally more than doubled between 1993 and 2000. Now, the Association represents all of the 149 accredited PA programs in the United States.