Burgess accepted an athletic scholarship to attend the University of Florida in Gainesville, Florida, where he swam for the Florida Gators swimming and diving team in National Collegiate Athletics Association (NCAA) competition from 1991 to 1994. While in college, he set four American records: two in the 200-meter individual medley and two in the 400-meter individual medley, and was a four-time NCAA champion in the same two events in 1993 and 1994. Burgess received twelve All-American honors as a Gator swimmer. He graduated from the University of Florida with a bachelor's degree in economics in 1994.
Burgess joined the U.S. Marine Corps in 1997, and has been promoted to the rank of major. In 2010, Burgess was inducted into the Marine Corps Sports Hall of Fame. Burgess has served two tours of duty in Iraq, and as the Chief of Mission for the U.S. military team at the international military games (CISM) for swimming in 2009 (Canada) and 2010 (Germany). He is one of a select few American Olympians to volunteer for military service.