The residency program at the Harvey & Bernice Jones Eye Institute began as a volunteer-led program in 1947, making it is one of the oldest ophthalmology training programs in the South. During this early period, residents were often trained by local volunteer faculty both on and off campus.

In 1969, the division of Ophthalmology became the department of Ophthalmology. Over the next decade, the residents were trained by full-time and part-time faculty members, conducted weekly education conferences, and participated in weekly problem case conferences.

In 1980, the addition of the annual Residents Day brought a new aspect to resident training, offering the opportunity to present research conducted throughout the last year. Residents Day also provided the opportunity for endowed lectureships and continuing education.

In 1981, the creation of the Accreditation Council for Graduate Medical Education (ACGME) brought about stricter standards and more oversight of resident education. Over the next 30 years, the residency at Jones Eye institute lived up to those standards by adding a full-time Residency Program Director, greatly increasing the amount of dedicated faculty educators, and developing curriculum to demonstrate seven learning competencies: patient care, medical knowledge, interpersonal and communication skills, professionalism, system-based practice, practice-based learning and improvement, and surgery.

In 1996, the department converted the program from a four-year program to a three-year program. In 2010 they began accepting three new residents each July, moving away from the staggered entry it once was. In 2017, the department added an international surgical rotation and updated to a state of the art surgical simulation lab.

Since the volunteer-led beginning, the department has graduated 160 residents (as of 2018) and currently admits four residents per year.