 Flagler attended Fernandina Beach High School, where as a senior he posted 1,683 rushing yards on 200 carries and 20 touchdowns, including one of the greatest games in Northeast Florida high school history, when against West Nassau (October 23, 1981) he had 405 rushing yards and 7 touchdowns.He also practiced basketball and led the district in scoring as a senior.He accepted a scholarship from Clemson University and became a full-time starter until his senior season.