The Academy was established in response to NASPA's initiative to provide continued professional education and development to meet the needs of vice presidents for student affairs, offering skill development in the areas of leadership and executive effectiveness.

In 1994, NASPA President James E. Scott appointed the Committee on Future Skills and Knowledge for Student Affairs Leaders, charging the committee with examining how VPSAs develop and refine professional skills throughout their careers and making recommendations on a deliberate process for continual professional development. The committee, consisting of VPSAs conducted a review of relevant theoretical constructs and applications affecting the future work of VPSAs and assessed pressing leadership effectiveness needs through extensive research and dialogue with VPSAs across the country.

By the end of 1997, the NASPA Board transformed the Committee on Future Skills and Knowledge into the National Academy for Leadership and Executive Effectiveness. On January 9, 1999, the Academy launched its first national Institute. In March 2003, the Academy was renamed in honor of past president James E. Scott.