Carter was born in Decatur, Georgia and had a stellar high school football career, becoming well-known in the Atlanta area. He originally signed a football letter of intent with Georgia Tech in 1996, but opted instead for baseball after being drafted by the Chicago Cubs. After two seasons in baseball, he went to the University of Georgia college football program in 1998. Carter won the starting job at Georgia in a tighly contested battle (over future Oklahoma starter Nate Hybl among others), and after an excellent freshman season, was recognized as one of the top young quarterbacks in NCAA football. He had a superb sophomore season but was mediocre as a junior due to injuries and inconsistencies. Carter declared himself eligible for the NFL draft after his junior season and was drafted by the Dallas Cowboys in the 2nd round as the 22nd pick of the 2001 NFL Draft.

Carter became the starting quarterback for the Dallas Cowboys team as a rookie, being part of a succession of short-tenured quarterbacks following the retirement of Troy Aikman. The highlight of his rookie season was a 20-13 victory over the New York Giants in which Carter threw for nearly 200 yards, scrambled for a key first down late in the game, and tossed the game-winning touchdown pass to veteran tight end Jackie Harris. Dallas would sign another young quarterback and former baseball player, Chad Hutchinson, following Carter's rookie season. He lost the starting job during his second season to Hutchinson after a loss to the Arizona Cardinals in which he engaged in a heated sideline discussion with Cowboys owner and general manager Jerry Jones. However, in his third season, under newly-hired head coach Bill Parcells, Carter retook the starting job and led the Cowboys to a 10-6 record and a playoff appearance. Hutchinson was released the next season after playing in NFL Europe.

Carter was released on August 4 of the 2004 offseason under unclear circumstances. The field of quarterbacks for the Cowboys in that offseason had expanded with the drafting of yet another former baseball player, Drew Henson and acquisition of Vinny Testaverde off of waivers; before Carter's release, it had been projected that Carter had a slight edge over Testaverde as the starting quarterback, and that former third-string quarterback Tony Romo would be released. Many believe Carter was released because of a failed drug test: However, the Cowboys' coach Bill Parcells insisted that, for reasons including but not limited to his drug problems, Carter could not be trusted with the leadership of the team. The official Cowboys statement regarding his release was a failed drug test, a poor attitude over the signing of Vinny Testaverde, and an average performance during the first week of training camp.

After being released by the Cowboys, Carter was signed to a one-year contract with the New York Jets, where he served as a backup to Chad Pennington and started three games (winning two) after Pennington suffered a rotater cuff injury. He suffered a drug relapse during the playoffs of the 2004 season, and has received treatement for drug addiction and recently-diagnosed bipolar disorder in Houston. The Jets released him during the 2005 offseason, and he currently lives in St. Louis, Missouri.

Carter's release by the Cowboys is currently subject to an arbitration hearing by the NFLPA. He officially filed his retirement papers in September 2005, but has stated he intends to return to the NFL.

Carter had success due to his athletic ability and specifically, his quickness and mobility. He is not blessed with the speed of a Michael Vick and in the NFL did not accumulate significant rushing yardage, but can be dangerous because of his ability to avoid rushers and buy time in the pocket. He also has an above average arm. He has been criticized for poor decision making on the field and lacking the passing accuracy neccessary for an NFL QB.

On April 4, 2006, Carter was signed by the Montreal Alouettes of the Canadian Football League to a one year contact with an option for 2007 only to be released by the team the following month.