He became club-captain under Eoin Hand, Ian Ross and Neil Warnock, he was Reserve Team Coach, along with Kevin Blackwell, in 1993 at Huddersfield until the end of the 1993–94 season.

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.

[4] His first game in charge ended in a 1–0 home defeat to former club Chester City three days later, when he had a disagreement with the referee at the final whistle resulting in a touchline ban.

[6] Lincoln won five of their six games in February to lift them clear of the relegation places and Jackson was named the League Two manager of the month.

[7] He was presented with his award in his final game before beginning treatment, when his side defeated Wycombe Wanderers 1–0 to lift them up to 14th in the table.

In June 2008, Jackson's doctors told him the treatment had been a success, but he will need regular check-ups until 2013, to ensure he does not relapse.

After a 1–0 loss in a Football League Trophy game to Darlington on 1 September 2009, Lincoln City parted company with Peter Jackson along with assistant Iffy Onoura.

[11] Jackson applied to succeed his former teammate Stuart McCall at Bradford City, the club where he started his career.

[13] In February 2011, Jackson was appointed as the interim manager of former club Bradford City, on a week-to-week basis, with David Wetherall as his assistant,[14] following the departure of Peter Taylor.

[citation needed] On 25 August 2011, Jackson offered his resignation to the club after a, "poor start to the season", and it was accepted.