Dr. Flynn received his medical degree with honors from Baylor College of Medicine in 1974 where he was elected AOA. He did his internship at Navy Hospital, San Diego followed by two years as a general medical officer which included a year as the physician for Operation Deep Freeze in Antarctica. Upon completion of his Navy obligation, he returned to Houston and completed his surgery residency at the University of Texas and remained as faculty until coming to the University of Florida in 1984.  Dr. Flynn rose through the ranks to become Professor of Surgery in 1994 and served as the General Surgery Residency Program Director from 1993 through 2003. He has training and Board certification in General Surgery, Vascular Surgery and Surgical Critical Care. In addition to his role as Surgery Program Director, he was Associate Dean for GME/DIO from 1992 through 2009.

Dr. Flynn has also served the Gainesville VA Medical Center as Chief of Surgical Services and held a number of appointments with the VA Headquarters in Washington. Dr. Flynn has won several awards including the Roche Award as Senior Medical Student from Baylor College of Medicine; the Navy Achievement Medal; the Outstanding Faculty Award from the University of Florida, General Surgery; and the Edward M. Copeland Chief Resident's Award, University of Florida. 

Dr. Flynn is the past chair of the American Board of Surgery and is currently Chair of the Accreditation Council for Graduate Medical Education board of directors. He is also Chair of the American College of Surgeons Board of Governors. He is listed in Best Doctor's in America, and Top Doctor by Castle Connolly Medical LTD. Dr. Flynn's clinical interests include dialysis access, limb salvage and complications from vascular interventions.