After taking the job, Gannon said that he hoped to bring in up to six players, most of them from England, to bolster a squad threadbare after summer exits. However, on the away leg in Wales, the "Steelmen" recorded a 3–0 win to send them into the next round. Motherwell then beat Flamurtari Vlorë 8–2 on aggregate after an 8–1 victory in the home leg. Motherwell were then knocked out by Romanian side FC Steaua București 6–1 on aggregate. Gannon was sent to the stand in Motherwell's Europa League match against Bucharest; However, Gannon later stated he did not know why he or his assistant manager were sent off by referee Carlos Clos Gómez. His first league victory was a 3–1 win over Kilmarnock at Fir Park.
Gannon was named Manager of the Month for October 2009, but he warned of a clear out in the January transfer window. His young team impressed, but proved to be inconsistent. Gannon had a dispute with the SFA head of referee development Hugh Dallas, following Gannon's criticism of Scottish referees. Gannon had claimed the standard of refereeing was "bringing the game into disrepute". He suggested a league table for referees. He then felt the official response to his criticisms to be disrespectful. Following this he temporarily refused to speak to the media, stating he did not wish to cause further controversy. He also criticised his predecessor Mark McGhee, after McGhee speculated in the press on possible transfers of Motherwell players. As well as this he had a public-falling out with club captain Stephen Craigan.
On 28 December, Gannon was dismissed by Motherwell, with the club indicating that Gannon was "not fully committed to the club" as the reason for their decision. He had been rumoured to be looking for other jobs. Dubbed a "loose Gannon", it was seen that either he or club captain Craigan would leave the club. Despite this he was praised for his signings from the English leagues, and for good open passing football his young side could play whilst at their best. The club lay bottom of the Championship, nine points adrift of safety. Gannon aimed to restore "pride" in the club, and offered a fresh start to unsettled players. He won his first game in charge, leading Peterborough to a 1–0 victory over Queens Park Rangers on 6 February. His contract was due to expire in the summer and the club were keen to tie him down to a longer deal. There soon came confusion over the exact role of the manager and others at the club in terms of recruiting new players.
He utilised unique tactical formations, which earned him comparisons to Martin O'Neill. He was particularly experimental with the front line, and was willing to use the loan market to bring in fresh talent. On 24 March, it was announced Gannon would leave Peterborough at the end of the season. Unable to avoid relegation despite a vast upturn in results, Gannon had been satisfied with the board's contract offer, but his family still resided in Stockport. He was replaced by Gary Johnson on 6 April, following Gannon's recommendation of Johnson, though Gannon insisted that this was not ultimately his decision but instead was down to the board. Striker Liam Dickinson was sad to see him go, and told the media that Gannon would have little trouble finding a new management post.
Port Vale
In January 2011, Gannon was one of three candidates reported to have impressed in interviews for the vacant Port Vale job, making him one of the favourites for the position. However, Paul Simpson's dismissal at Stockport County led to hopes of a return to the club for some County fans. Therefore, he was installed as the bookmakers' favourite to become the next Port Vale manager, and also the bookmakers' favourite for the Stockport job. Gannon was confirmed as the manager of Port Vale on 6 January 2011, succeeding Micky Adams at the helm of the promotion chasing club, signing a contract that lasted until summer 2012. Saying that finishing outside of the top seven would be a "failure", Gannon's first task after "burying the hatchet" with Gareth Owen was to look for a new striker. Two weeks into his reign club captain Tommy Fraser left the club by mutual consent, as signs of what would be an unhappy relationship between club and manager quickly came to the surface. Gannon then brought in Romaine Sawyers and Kayleden Brown on loan from West Bromwich Albion, Jay O'Shea on loan from Birmingham City, Exodus Geohaghon on loan from Peterborough United, and striker Tom Pope on loan from Rotherham United.
Losing four of his first five games in charge, Gannon was forced to respond to criticism over his team selections and substitutions, and announced plans to expand the club's non-playing staff. On 1 February the players met with the chairman and rumours spread that Gannon had 'lost the dressing room', as comparisons were made with Brian Clough's Leeds United tenure from The Damned United. Yet the next day an O'Shea volley gave Vale a 1–0 win over promotion rivals Rotherham United to give Gannon his first win in charge at the club. However, tension remained, as proven at the end of the month when it was reported that Gannon left the team bus on a pre-match journey after rowing with assistant manager Geoff Horsfield. Gannon had previously told the press his staff were "underqualified", though insisted any changes would be "implemented at a later stage" and that Horsfield was a "great assistant".
It was later reported in the media that Horsfield had requested a day off to deal with a family matter, which Gannon granted before subsequently writing a letter to the board complaining of Horsfield's conduct. An unnamed director then handed the letter to Horsfield, who confronted Gannon over the issue and brandished the letter as proof when Gannon denied its existence. This came on the same day that local newspaper The Sentinel ran an editorial that questioned Gannon's loan signings, his decision to drop Gary Roberts and branded his tactics and team selections as "baffling". Having returned to the team to steer his side to a 2–1 victory over Aldershot Town, Gannon said "there's been misrepresentation in the media over my part in this. I'm completely the innocent party". The club informed Horsfield that he would face a disciplinary hearing, whilst Gannon would not be asked to defend his actions and would merely provide a witness statement. The club took no action, and after Horsfield spent two weeks at home the pair returned to work as before. He continued to exploit the loan market, signing Dominic Blizzard from Bristol Rovers, a midfielder who played under him at Stockport.
Vale's poor form continued and on 19 March they dropped out of the play-off places for the first time all season following a 3–0 defeat at Accrington Stanley. Ugly post-match scenes at the Crown Ground saw Geohaghon confront fans who singled him out for abuse, whilst Gannon was ushered quietly out of the back door. Roberts told the media "I don't think the manager likes me and, to be honest, I don't like him". Rumours circulated that Gannon would soon be on his way out. These rumours were proved accurate two days later, as Gannon's departure was confirmed by the club. Deeply unpopular with Vale supporters, his sacking was "quick and with little emotion", whilst his reported poor man-management skills resulted in him having the shortest reign as manager in the club's history. Despite this he did receive credit for spotting the potential talent in a teenage Sam Morsy, and for bringing Tom Pope to the club. Gannon himself made a statement on his website declaring his disappointment in the club's decision to terminate his contract after such a short period of time, and also bemoaned that he "wasn't able to add many new players [to the squad]". Port Vale continued to struggle under caretaker manager Mark Grew, winning just two of their remaining ten games, and finishing 2010–11 in 11th place.
Return to Stockport County
thumb|Gannon as [[Stockport County F.C.|Stockport County manager in 2012]]
Following the resignation of Dietmar Hamann in November 2011, speculation came of a return to Stockport County for Gannon; when questioned on the possibility, club chairman Peter Snape stated that should he apply for the position then "he'd merit very serious consideration". In the thirty months since Gannon's departure, the club had seen five full-time managers come and go, suffered relegation into the Conference National and had not won back-to-back games since February 2009. On 14 November, he was revealed as the club's director of football, a position leaving him "responsible for all football matters including 1st team selection and transfers"; Willie McStay remained at the club, as his assistant. When he took charge Stockport were 17th in the league, just two points above the relegation zone, having won just three of their opening twenty games. He stated that his aim for 2011–12 was to avoid letting the club slip to a third-successive relegation.
After losing his first five games in charge, including a 7–0 defeat against Grimsby Town at Blundell Park, Gannon said that the club's finances limited his ability to change personnel. He also stated that "if I didn't take the job, this club would've had a real chance of dying... I'm not proud to be the manager of a club that loses 7–0... but this is my team now... It has always been my club, so it's my responsibility to make things better, and over time we will." defender Chris Blackburn, and seven goal top-scorer Nick Chadwick in the January transfer window. He then signed defender Joe Connor on non-contract terms, and teenagers Aaron Cole and Danny Rowe on loan. His first win in his second spell at the club came on New Year's Day, in a 3–2 victory over Barrow at Edgeley Park. He then re-signed former players Paul Turnbull and Matty Mainwaring on loan. Worried by the situation at crisis clubs Darlington and Kettering Town, Gannon cancelled the contracts of veterans Matt Glennon, John Miles, Mark Lynch, and Ryan McCann. He brought in 23-year-old Telford defender Sean Newton and 18-year-old Sunderland keeper Lewis King on loan, whilst signing 19-year-old Lancaster City midfielder Danny Hattersley on a permanent transfer. The "Hatters" secured their Conference status with two games to spare, after a 1–1 home draw with Braintree Town on 14 April, having lost just twice in the league at Edgeley Park since Gannon's return. Stockport finished the campaign in 16th place, 10 points above the drop and 20 points below the play-off zone.
In preparation for the 2012–13 season, Gannon signed defenders Sean Newton and James Tunnicliffe, and took back Paul Turnbull on loan once again. However, he was disappointed to lose striker Tom Elliott, who rejected a contract offer to switch to Cambridge United. He also appointed long-time associate Alan Lord as his assistant. However, County found themselves struggling in the league, and Gannon blamed the predicament on the board's decision to slash the wage budget in the summer. An angry Lord Snape told the press that "I'm getting pretty fed up of watching part-time teams beat Stockport County. Changes are going to be made unless things improve. Jim Gannon's pretty good at telling me how this club should be run. Well I'm going to tell him that I'm not impressed by the way the team is being run. If we lose a couple of our next games, we're in a relegation battle with a much bigger budget than most of the teams down there with us, which quite frankly is not good enough." 14 months into his second spell at Edgeley Park and with County sitting in the relegation zone, Gannon was relieved of his duties as Stockport manager on 16 January 2013 following the 3–1 home defeat by Mansfield Town.
Northwich Victoria
On 9 December 2013, it was announced that Gannon would become the new manager of Northern Premier League Division One North side Northwich Victoria. He replaced Lee Ashcroft, who resigned as manager and became director of football after picking up a ten-match ban for sexist abuse. The "Vics" ended the 2013–14 season in ninth place. They reached the play-offs in the 2014–15 campaign, losing to Bamber Bridge at the semi-final stage. He took the club on a successful FA Cup run in the 2015–16 campaign, leaving them as the lowest rank team in the competition when they were knocked out by League Two side Northampton Town in the second round. Northwich had led 2–0 with eight minutes to play before a late comeback from Northampton.
Third spell at Stockport County
Gannon became manager of Stockport County, now in the National League North, for the third time in his career on 18 January 2016. Gannon started well, taking the team to the Cheshire Senior Cup final and up to ninth in the table with a sequence of seven games unbeaten, including five victories, in the run-up to Easter. In December, he signed a new two-and-a-half-year contract. County finished eighth in the 2016–17 season, one point outside the play-offs. Gannon was credited with turning around the career of Danny Lloyd, who signed for Peterborough United in May 2017, 12 months after Gannon had persuaded him to play for County rather than quit the game altogether. Gannon said that he was pleased with his defence, but wanted to overhaul the attacking side to reach the play-offs the following season. He achieved his aim as Stockport qualified for the play-offs with a fifth-place finish in the 2017–18 campaign, before losing 1–0 to Chorley in the qualifying round. Following the defeat he sold 22-year-old midfielder James Ball to Stevenage for an undisclosed five-figure fee.
County reached the second round of the FA Cup in the 2018–19 season, where they fell to a 1–0 defeat at Barnet. Gannon was named as Manager of the Month award in the National League North for December 2018 after his team rose from the bottom half of the table to the top three and also advanced in the FA Trophy. They went on to finish as champions, beating Chorley into second-place by a single point, to end a six-year stay in the sixth-tier. He was named as National League North Manager of the Year for the 2018–19 season. Stockport were just inside the play-offs in seventh-place in the National League when the 2019–20 season was postponed, never to be resumed, on 26 March. Stockport were denied a play-off place However, as they dropped to eighth-place on points-per-game. On 21 January 2021, with the club sitting fourth in the National League, Stockport parted company with Gannon, the board citing that "the decision is not results based but is centred around culture". In July 2021, he was appointed as Football Education Programme Manager at Oldham Athletic.
Hyde United
On 31 August 2021, Gannon was announced as the new manager of Northern Premier League Premier Division side Hyde United. He stated: "I am not coming in to change things but embrace the philosophy that is already here and the way they play and develop it." On 10 February 2022, Gannon was sacked with Hyde sitting 19th in the league table, one place above the relegation zone.
Managerial style
Gannon holds a full UEFA Pro Licence.
Priding himself on playing flowing football in the lower leagues of the English game, Gannon has repeatedly spoken out against clubs he feels play too physically and referees he feels do not give his players enough protection. As a manager in England, Scotland and Ireland, his teams have picked up fair play awards. He has stated that this fair play approach is based on his belief that it is "good principles that lead to good football".|Gannon speaking in February 2010.
Gannon has also been called a "tactical maverick" due to his unusual formations. These formations include 3–4–1–2, 4–3–2–1, 4–1–2–3, and his preferred set-up of 4–2–3–1. He has stated that he prefers formations that use four lines of players (as opposed to three lines in the classic 4–4–2) due to the added depth in defence and presence in midfield, and was inspired to use the formations by Carlo Ancelotti. He is known to be extremely thorough and meticulous in preparing his players for games.
Of an outspoken nature, he has had public fallings out with players, referees, chairmen, opposition players and managers, and authorities. The Guardian surmised this by saying that "the feeling about Gannon is that it is his way or the highway."
Career statistics
Playing statistics
{| class="wikitable" style="text-align: center;"
|+ Appearances and goals by club, season and competition
|-
!rowspan="2"|Club
!rowspan="2"|Season
!colspan="3"|League
!colspan="2"|National cup
!colspan="2"|Other
!colspan="2"|Total
|-
!Division!!Apps!!Goals!!Apps!!Goals!!Apps!!Goals!!Apps!!Goals
|-
|rowspan="3"|Dundalk
|1987–98
|LOI Premier Division
|2||0||0||0||1||0||3||0
|-
|1988–99
|LOI Premier Division
|26||1||2||0||6||0||34||1
|-
!colspan="2"|Total
!28!!1!!2!!0!!7!!0!!37!!1
|-
|Sheffield United
|1989–90
|Second Division
|0||0||0||0||0||0||0||0
|-
|Halifax Town (loan)
|1989–90
|Fourth Division
|2||0||0||0||0||0||2||0
|-
|rowspan="12"|Stockport County
|1989–90
|Fourth Division
|7||1||0||0||1||0||8||1
|-
|1990–91
|Fourth Division
|41||6||1||0||4||1||46||7
|-
|1991–92
|Third Division
|43||16||2||1||13||4||58||21
|-
|1992–93
|Second Division
|46||12||3||0||14||3||63||15
|-
|1993–94
|Second Division
|16||0||2||0||4||1||22||1
|-
|1994–95
|Second Division
|45||7||1||0||6||0||52||7
|-
|1995–96
|Second Division
|23||1||2||0||7||1||32||2
|-
|1996–97
|Second Division
|40||4||4||0||15||1||59||5
|-
|1997–98
|First Division
|36||1||0||2||0||4||42||1
|-
|1998–99
|First Division
|38||0||2||0||2||0||42||0
|-
|1999–2000
|First Division
|29||0||1||0||3||0||33||0
|-
!colspan="2"|Total
!383!!52!!20!!1!!77!!11!!480!!64
|-
|Notts County (loan)
|1993–94
|First Division
|2||0||0||0||0||0||2||0
|-
|Crewe Alexandra
|2000–01
|First Division
|7||0||3||0||0||0||10||0
|-
|rowspan="4"|Shelbourne
|2001–02
|LOI Premier Division
|30||4||1||0||1||0||32||4
|-
|2002–03
|LOI Premier Division
|22||4||1||0||2||1||25||5
|-
|2003
|LOI Premier Division
|9||1||0||0||0||0||9||1
|-
!colspan="2"|Total
!61!!9!!2!!0!!3!!1!!66!!10
|-
!colspan=3|Career total
!455!!61!!25!!1!!50!!12!!560!!74
|}
:A. The "Other" column constitutes appearances and goals in the League Cup, Football League Trophy, Football League play-offs, Full Members Cup, LFA President Cup, Leinster Senior Cup, League of Ireland Cup, and UEFA Champions League.
Managerial statistics
{| class=wikitable style="text-align: center"
|+ Managerial record by team and tenure
|-
!rowspan=2|Team
!rowspan=2|From
!rowspan=2|To
!colspan=5|Record
!rowspan=2|
|-
!!!!!!!!!
|-
|align=left|Dundalk
|align=left|8 June 2004
|align=left|14 November 2005
|
|-
|align=left|Stockport County
|align=left|28 December 2005
|align=left|6 May 2009
|
|-
|align=left|Motherwell
|align=left|30 June 2009
|align=left|28 December 2009
|
|-
!colspan=3|Total
|}
Honours
As player
Dundalk
- LFA President Cup: 1989; runner-up: 1988
- National League North: 2018–19
Northwich Victoria
- Cheshire Senior Cup: 2013–14
Individual
- Scottish Premier League Manager of the Month: October 2009
- National League North Manager of the Year: 2018–19