In 1999, the National Security Agency (NSA) launched the Center of Academic Excellence in Information Assurance Education (CAE-IAE) program. Under this program, an institution could receive the CAE-IAE designation if it passed rigorous curriculum and program requirements. Seven schools received designation by May 1999, and not long after, more institutions began to join the ranks of CAE designated institutions. While the CAE-IAE program initially formed to address the shortage of intelligence community professionals, the program later expanded to address the shortage of qualified cybersecurity professionals in the workforce.

In 2004, the Department of Homeland Security (DHS) became a co-sponsor of the CAE-IAE program. In addition to adding a co-sponsor, the CAE-IAE program had several changes to the program including adding the CAE-Research  (CAE-R) designation in 2008, adding a designation pathway for two-year colleges in 2019, and a name change for the program to the CAE in Cyber Defense Education (CAE-CDE) in 2017.

Today, the National Centers of Academic Excellence in Cybersecurity (CAE-C) program has over 300 institutions all over the Nation with designations in Cyber Defense, Research, and Cyber Operations.