The Flagler Trail is located along an abandoned railroad known as the Okeechobee Branch of the Florida East Coast Railway that later came to be known as State Road 13. The corridor was never used as a road, however, and the railroad was eventually abandoned in the fifties. The right-of-way was acquired by Seminole County in 1984 from the Florida Department of Transportation and was restricted to public use. Around 1975, the Florida Trail Association designated the southern portion of the trail as a part of the Florida National Scenic Trail, a designation that is given by the U.S. Congress based on the length and scenic quality of a trail. It has been functioning as a public wilderness trail ever since.

Map of the Flagler Trail