Jackson attended the University of Notre Dame, where he was a two-year starter and set school single-season records for passing yards (2,753), completions (184), and attempts (316) as a senior during the 1999 season. In the process, he broke the yardage mark held by the legendary Joe Theismann. (All of Jackson's records were subsequently broken by Brady Quinn.) Jackson also threw for 17 touchdowns during his senior year, ranking third behind Ron Powlus and Rick Mirer. He was second on the team in rushing with 140 carries for 464 yards (3.3 avg) and 7 scores.
Jackson was drafted in the 7th round of the 2000 NFL Draft, 214th overall, by the Denver Broncos. Pro scouts projected that Jackson could develop into a solid NFL quarterback if placed into the right system. However, after four seasons as a Bronco backup, he saw action in only five games, completing 11 of 22 passes for 114 yards.
In 2004, Jackson signed onto the practice squad of the BC Lions in the CFL. He began 2005 on the practice squad, but was elevated to the active roster when CFL superstars Dave Dickenson and Casey Printers went down with injuries. He saw action in 2 games, had 3 completions out of 6 attempts for a total of 30 yards and rushed four times for a total of 35 yards.
At the beginning of 2006 season, Jackson began as the third-string quarterback, behind Dickenson and Buck Pierce. However, with alternating injuries to Dickenson and Pierce, he made appearances in all but the final regular season game.2007 proved, however, to be Jackson's break-out season as he became starting quarterback when Dickenson and Pierce were both out with injuries. For the 11 games Jackson was starting, he had a record of 9–2, threw for 2,553 yards, 18 TDs on 167 completions and 10 interceptions. On February 4, 2008, Jackson re-signed with the Lions 12 days before qualifying as a free-agent. At the beginning of the 2008 season, he was the back-up to Buck Pierce, but has started some games. His only pass in the Western semi-final was a touchdown toss to Geroy Simon.
He was released by the Lions on February 1, 2012.
On February 22, 2012, it was announced that Jackson had signed a two-year contract with the Toronto Argonauts. He dressed in all 18 games, starting in four, and was a member of the 100th Grey Cup winning team while throwing a touchdown pass in that game. On February 4, 2013, he was released by the Toronto Argonauts.
Shortly after his release from the Argonauts, it was announced that Jackson would sign a one-day contract with the BC Lions so that he could retire as a Lion.
Immediately upon retiring it was announced that Jackson would then begin his coaching career as the quarterbacks coach for the Lions. After coaching in BC for one year (2013) he spent the next couple seasons as the quarterbacks coach for both the Edmonton Eskimos and Saskatchewan Roughriders before being named the BC Lions' Offensive Coordinator for the 2018 season.