The Brigham Young University Studies organization was created in 1959 by a group of scholars whose mission was to produce scholarly religious literature. This organization was placed under the direction of the College of Humanities from 1982 to 1993. While in the College of Humanities, the BYU Studies journal was directed by the journal editor, who was under the direction of the college dean. The administrative structure of the organization consisted of an editorial board composed of from various disciplines review submissions, assign peer reviewers, and plan upcoming events. An advisory board provides long-term vision and planning through its quarterly meetings. The organization is also influenced by the Academy, composed of one-hundred scholars from BYU and the larger LDS community who voluntarily work to promote LDS scholarship at BYU Studies. In 1993, BYU Studies left the College of Humanities and became part of the Associate Academic Vice President’s office, first under the direction of Gary Hooper, then Brent Webb.

In 2006, BYU Studies became part of the Neal A. Maxwell Institute for Religious Scholarship with M. Gerald Bradford functioning as Executive Director. Once the journal became associated with the Neal A. Maxwell Institute for Religious Scholarship, the Executive Director acted in the same capacity as a Dean of an academic department and the Director of BYU Studies and Editor-in-Chief functioned in the same capacity as a Department Chair. From its inception in 1959 the chief editors included Clinton F. Larson (1959 to 1967), Charles D. Tate, Jr., (1968 to 1983), Edward A. Geary, Jr. (1984-1991), and John W. Welch (1992- ).