Leeds United youngster Mark Jackson came to Carrow Road on trial in early December 1999, available on a free transfer. The 22 year old who can play in either defence or midfield, had made 19 appearances for Leeds. He made his debut under Howard Wilkinson but most of his appearances came under George Graham in 1996/97. He also made 5 appearances whilst on loan to Huddersfield in 1998/99.

Mark played for the Reserves alongside fellow triallist Michael Stephen in the 2-2 draw with Leyton Orient on 7th December 1999. After a poor performance in the Reserves' defeat by Gillingham in January 2000, Bruce Rioch decided not to take Mark on.

According to Ceefax, Mark joined Barnsley on loan on 13th January 2000. After a month, he returned to Leeds but immediately began interesting other sides. Bristol Rovers manager Ian Holloway commented that "Mark looks good but he's on a lot of money". As Rovers had a surplus of right sided centre backs, Holloway decided not to pursue this move. Teamtalk then reported on Thursday 24th February 2000 that Mark was at Scunthorpe negotiating a move and that a fee had been agreed. However this was scuppered by a late bid by John Benson's Wigan and Mark played as a triallist for them in a Reserve match against Chesterfield. Preston North End were also said to be interested. After a spell of flu, Mark finally signed for Scunthorpe on 9th March 2000.

On October 5th 2004, Conference side Carlisle United made a bid to bring Jackson to Brunton Park on loan.

On 13th February 2005, Mark joined Kidderminster Harriers on a contract until the summer of 2006. Although he had made over 150 appearances for the Iron, he had not hardly figured in their first team this season following injury. Scunthorpe manager Brian Laws recognised that Mark needed first team action and so let him go. Harriers boss Stuart Watkiss was pleased to add Jackson to his squad, as Kidderminster are four points adrift of safety at the foot of the table. "It's no secret that our defensive record has been poor this season and we are still making too many errors, that is why I have brought Mark in, He was a regular at Scunthorpe for four years until he got injured last season, he knows what the game is about at this level. He's a good, hard defender who doesn't complicate things"

Along with teammate Iyseden Christie, Mark returned to league football on 31st January 2006 joining Rochdale for a combined fee of £35,000.

Jackson remained at Rochdale, making a total of 26 appearances, until the end of the 2006/7 season when he was one of two players not to have their contracts extended (the other being striker Clive Moyo-Modise). Mark joined Blue Square Premier (the new name for the Conference) newboys Farsley Celtic in June 2007.

He became the manager of the Under-19s team which were formed at the start of the 2008–09 season. When his first team manager, John Deacy was sacked, Neil Parsley took over and Jackson became the first team assistant manager.

In November 2015 he rejoined Leeds as their Under 15s/Under 16s coach. He then progressed to managing the Under-16s, Under-18s (winning the Professional Development Northern League in 2017/18) and Under-23s. In March 2022 he was appointed as first team coach working under new Leeds manager Jesse Marsch. On 23rd December 2022 he was appointed manager of MK Dons replacing Liam Manning.

Jackson was sacked by the MK Dons on 9th May 2023 following their relegation to League Two. They were relegated following the 0-0 draw with Burton on 7th May 2023. Jackson had said he wanted to remain as manager for next season immediately after that game. However, a short Dons statement  on Tuesday confirmed his departure, thanking Jackson, Stockdale and analyst Aaron Dagger, who is also leaving the club, "for their efforts during their time at Stadium MK".

On 27th September 2023 he was appointed manager of Australian side Central Coast Mariners. In his first campaign they won the Australian FA Cup and the A-League Premiership, beating Melbourne Victory 3-1 in the Grand Final on 25th May 2024. He was named Coach of the Year.