In the 1960s, UCSF (then called the Medical Department of the University of California) gained more independence from the UC system.

The four departments (Medicine, Pharmacy, Dentistry, and Nursing) were renamed as "school of", and the Graduate Division was founded in 1961.

At the time of its creation, the UCSF Graduate Division offered graduate programs in anatomy, biochemistry, comparative biochemistry, biophysics, dental surgery, dentistry, endocrinology, history of medicine, medical physics, microbiology, nursing, nutrition, pathology, comparative pathology, pharmaceutical chemistry, pharmacology, comparative pharmacology and toxicology, physiology, and animal physiology.

In 1969, the School of Medicine and the Graduate Division sponsored the creation of the Medical Scientist Training Program (MSTP).

This program, funded by the US Public Health Service, offers a special stipend to students to pursue graduate work along with a medical degree, in order to address the lack of research training in physicians.