The Honors Program was established by university president Ernest L. Wilkinson in 1960 to broaden and enrich the undergraduate student experience through intensive general education courses. The Honors Program has been associated with various units of the university administration. Initially it reported directly to university administration, then in 1973 was placed under the dean of College of General Studies. In 1979 it was again placed under the direction of the university, but after 1983 began reporting through the dean of General Education and Honors and the dean of Undergraduate Education. As of 2023, the program was still active.

The General Education and Honors administrative body was formed at Brigham Young University in 1986, when General Education and University Honors Education were placed under the leadership of one administrator, known as the Dean of General Education and Honors, who reported directly to the university. This continued until 2002 when the name was changed to Undergraduate Education, which reflected its main focus. Deans of General Education and Honors included: James R. Kearl (1986-1989), Harold L. Miller, Jr. (1989-1993), Paul A. Cox (1993-1997), James E. Faulconer (Acting Dean, 1997-1998; Dean, 1998-2000), George S. Tate (2000-2002). General Education and Honors oversaw the GE component of a BYU education as well as the Honors Program. At various points in its existence, the administration also supervised First-Year Writing, Freshman Academy, the Freshman Year Office, and Pre-professional Advisement.