Born in the Hell's Kitchen section of New York City, Flynn attended Fordham University, where he earned a BA and an MBA degree in finance. He worked for the New York Racing Association for 18 years – his last six years as assistant racing secretary – before joining the New York Horsemen's and Benevolent Association, the forerunner of the NYTHA, as its executive director in 1994. A past winner of the New York Turf Writers Association's Red Smith "Good Guy" Award, Flynn and his wife, Judy, live in West Hempstead, NY.
Robert F. Flynn has been named to the Board of Trustees of the New York Racing Association. The appointment is subject to the approval of the New York State Racing and Wagering Board. Flynn, 50, is the executive director of the New York Thoroughbred Horsemen's Association. Flynn said. "I think this is going to be very positive for all concerned – for NYRA, for the horsemen and for myself – especially in terms of communication with all aspects of our industry."