Huddersfield Town Jackson returned to Huddersfield Town when they gave him the opportunity to become manager in October 1997 replacing
Brian Horton, after spending a few weeks playing for neighbours
Halifax Town and putting them on course for a return to
the Football League. He was assisted at Huddersfield by former
Welsh manager
Terry Yorath. In his first two seasons in charge he helped Town avoid relegation, and helped them to 10th place in
Division One. However, he was controversially sacked by owner Barry Rubery in 1999 to make way for
Steve Bruce.
Return to Huddersfield Town In 2003, Jackson was re-appointed manager of a Huddersfield Town that had slid down to
Division Three and were emerging from administration. In the
2003–04 season, Jackson put his faith in a squad containing promising young players. Town finished fourth to gain a place in the play-offs. Town eventually beat
Mansfield Town on penalties in the play-off final to be promoted in Jackson's first season back. The
2004–05 season saw Town finish ninth, just missing out the play-off places for promotion to the
Championship. Town had a great start to the
2005–06 campaign with Jackson winning Manager of the Month for August 2005 and after eventually finishing fourth and making the League One Play-Offs, they lost 3–2 to
Barnsley on aggregate. On 18 May 2006, he signed a two-year extension to his contract that would have seen him managing the club until 2009. Jackson was sent to the stands on 12 August 2006 after grabbing
Bristol City's
Lee Johnson around the throat in a touchline altercation 10 minutes from time in Huddersfield's 2–1 win over Bristol City. On 30 August 2006, it was announced that
the Football Association would charge Jackson over the incident and Jackson said he would appeal against the charge. He lost the appeal, but was forced to pay
£300, rather than serve a touchline ban. On 6 March 2007, Jackson left Huddersfield with his contract cancelled by mutual consent. Jackson's last game in charge was a 5–1 defeat to
Nottingham Forest on 3 March 2007. A statement from the board said: "The Board's clearly stated minimum aim at the start of the season was to achieve a Play-Off position, but unfortunately due to our form and the inability to attract key players, this objective is now looking remote."
Lincoln City On 30 October 2007, Jackson was appointed as manager of
League Two side
Lincoln City who were bottom of
the Football League. The Lincoln board cited the club's poor home form over the previous season and poor start to the present season as reasons for their decision. Jackson applied to succeed his former teammate
Stuart McCall at Bradford City, the club where he started his career. He was shortlisted for the vacancy but the board appointed
Peter Taylor instead of Jackson. In March 2010, he joined his wife Alison, as a director of home care franchise Caremark Calderdale which provides care at home for elderly and disabled people as well as people with terminal illnesses across Calderdale. The couple will run the franchise from the Elsie Whiteley Innovation Centre, Halifax. following the departure of
Peter Taylor. Jackson later announced that his permanent assistant would be former Middlesbrough FC assistant manager,
Colin Cooper. During the summer, Jackson was given the position of permanent manager on a one-year contract for the
2011–12 season. Cooper also signed a one-year contract to continue as Jackson's assistant. On 25 August 2011, Jackson offered his resignation to the club after a, "poor start to the season", and it was accepted.{{cite web ==Managerial statistics==