Kelly joined the University of California, San Francisco (UCSF) in 1971. He began as an assistant professor in the Department of Biochemistry and Biophysics. His neurobiology research explored biochemical mechanisms of synaptic transmission and neural plasticity involved in long-term memory.[4]
While at UCSF Kelly was appointed chair of the Department of Biochemistry and Biophysics (1995–2000), director of the graduate program in Cell Biology (1988–1995) and director of the Hormone Research Institute (1992–2000).[5]
During this time he served on the editorial boards of scientific journals, including Cell, The Journal of Cell Biology, The Journal of Membrane Biology, Trends in Neurosciences, and Traffic. He also served on the national committee for the Council of American Society for Cell Biology from 1989 to 1992.
In 2000 Kelly was appointed executive vice-chancellor of UCSF. As chancellor he directed the construction of the new UCSF Mission Bay Campus and oversaw the UCSF research enterprise.[6]
As director Kelly's stated goal is to promote academic research as a means to improve public health and drive economic growth. To accomplish this he bridges academia with commercial industries and entrepreneurship ventures.[3][7]
In addition Kelly, with QB3's associate director Douglas Crawford, created the first startup incubator at the University of California—the QB3 Garage, which has expanded into a network of five incubators hosting over 40 companies.[8] Under Kelly's direction QB3 has initiated Bridging-the-Gap Awards and the Start-up-In-A-Box Program to fund translational research and provide resources for start-up ventures with the potential for commercialisation.[9][10]