Hayden was born in Owensboro, Kentucky. He started road racing with the CMRA, often against racers many times older. Hayden would often start races from the back of the grid because a family or crew member would have to hold his bike upright as his feet would not yet touch the ground. Later, at age 17, he was racing factory Honda RC45 superbikes while still in high school. In 1999, he won the AMA Supersport championship on board a privateer Honda. In 2001, his first full season as an AMA superbike racer, he came within 40 points of winning the championship, finishing behind only champion Mat Mladin and runner-up Eric Bostrom. The 2002 season, however, would see Hayden answering the bell: he won the Daytona 200 on a Honda Superbike en route to becoming the youngest ever AMA Superbike Champion, defeating reigning triple champion Mat Mladin, among others. He also entered the World Superbike round at Laguna Seca, making a solid 4th in the first race before colliding with Noriyuki Haga in race two.