Thornton attended LaGrange High School, where he was a three-year starter at running back. As a senior, he earned Super PrepAll-America honors after finishing with 1,920 rushing yards, 28 touchdowns, 932 return yards and 12 blocked kicks. In his high school career he totalled 560 carries for 4,541 rushing yards. He accepted a football scholarship from the University of Georgia. He redshirted his freshman year after breaking his thumb. The following season, he only started one game at tailback, registering 230 yards, 47 carries, 3 touchdowns, while averaging 18.4 yards per kickoff return. As a sophomore, he was converted into a cornerback by Willie Martinez, Georgia's secondary coach and defensive coordinator. He had 9 starts, while collecting 32 tackles, one tackle for loss and 7 passes defensed. As a junior, he collected 43 tackles, 4 tackles for loss, 2 interceptions, 6 passes defensed. He returned a blocked punt 12 yards for a touchdown against Northwestern Louisiana State University. He also returned an interception 71 yards for a touchdown in the Sugar Bowl against Florida State University. As a senior, he was named a team captain and was the Bulldogs' best cornerback, starting 13 games and often facing the opponents' best wide receiver. He posted 54 tackles, 3 tackles for loss, 8 passes defensed and 2 interceptions. He finished his college career with 129 tackles, 4 interceptions, 21 passes defensed, 41 carries for 230 yards, 3 touchdowns and 22 kickoff returns for 404 yards. as a sophomore …
Thornton was selected by the Dallas Cowboys in the fourth round of the 2004 NFL Draft. He only apppeared in one game, in which he returned two kickoffs for 43 yards, before tearing his ACL. He was placed on the injured reserve list on October 12. He was waived on September 8, 2005.
On September 14, 2005, the San Francisco 49ers signed him to their practice squad. Injuries forced the 49ers to promote him to the active roster on October 2 and eventually named him the starter at left cornerback. In his first start he was matched against All-ProMarvin Harrison, and was able to limit him to 2 receptions for 17 yards. He also intercepted quarterback Peyton Manning in the end zone, and received honorable-mention NFL defensive player of the week honors for his efforts. He appeared in 12 games with 11 starts, finishing with 32 tackles, 2 interceptions and 8 passes defensed. On August 1, 2006, he was released after struggles in his play caused him to drop on the depth chart.
