During the 2005–06 English football season, Gillingham F.C. competed in Football League One, the third tier of the English football league system. It was the 74th season in which Gillingham competed in the Football League and the 56th since the club was voted back into the league in 1950. It was Gillingham's first season in the third tier of the English league system since 2000, following the team's relegation from the Football League Championship at the end of the previous season.

Prior to the season, Neale Cooper was appointed as the club's new manager, but after a poor start to the campaign he resigned from the role in mid-November with Gillingham in 22nd place out of 24 teams in the league table, a position which if maintained would result in relegation to Football League Two at the end of the campaign. His assistant, Ronnie Jepson, was appointed on a temporary basis but ultimately remained in the role for the remainder of the season. The team's results quickly improved, and they had climbed to 17th place by the end of 2005. Although a lengthy run without a win in February and March, culminating in a 6–0 defeat to Bristol City, led to Gillingham slipping back to 21st place and once again being in danger of relegation, they then won six consecutive games and ended the season in 14th place.

The club also competed in three knock-out tournaments. In the FA Cup, they were defeated in the first round by Burscough, a team playing in the seventh tier of English football, in what was seen as a shock result. In the Football League Cup, Gillingham defeated Portsmouth of the top-tier FA Premier League before being eliminated in the third round. They also reached the second round of the Football League Trophy. Gillingham played 52 competitive matches, winning 19, drawing 13, and losing 20. Darren Byfield was the team's top goalscorer with 14 goals. Andrew Crofts made the most appearances, missing only one game. The highest attendance recorded at the club's home ground, Priestfield Stadium, was 8,128 for a league game against Southend United in October.

Background and pre-season The 2005–06 season was Gillingham's 74th season in the Football League and the 56th since the club was re-elected to the League in 1950 after being voted out in 1938. At the end of the previous season, Gillingham had been relegated from the Football League Championship after finishing 22nd out of 24 teams in the league table, ending a five-year spell in the second tier of the English football league system and meaning that they would compete in Football League One, the third tier, in the 2005–06 season.

On 21 May, Neale Cooper was appointed as the club's new manager, replacing Stan Ternent, who had resigned on 15 May. Ronnie Jepson, who had served as assistant manager to Ternent, remained in the role; he had reportedly been considered for the manager's job himself. Bobby Paterson, who had worked with Cooper at the manager's previous club, Hartlepool United, joined Gillingham in the dual roles of director of youth and manager of the reserve team. There was considerable change in Gillingham's playing squad following the club's relegation. Darius Henderson, the team's top goalscorer in the previous season, moved to Watford for a transfer fee of £450,000. Paul Smith, who had been the team's captain during the previous season and played nearly 400 games in eight seasons with Gillingham, left the club after turning down a new contract which would have seen his wages dramatically reduced. Barry Ashby, who had also been with Gillingham for eight years and had made over 300 appearances, left the club at the expiration of his contract, as did Nicky Southall, Nyron Nosworthy, Mamady Sidibé and John Hills, all of whom had been regulars in the team during the previous campaign. Of 12 players whose contracts had expired at the end of the 2004–05 season, only two opted to re-sign with the club.

Cooper signed four new players ahead of the first match of the new season, including two who had last played in his native Scotland: Paul Shields, a forward who joined Gillingham from Forfar Athletic, and Tony Bullock, a goalkeeper who had come to the end of his contract at Dundee United. Shields was still under contract at Forfar; the club had reportedly received interest from at least four clubs for him, but ultimately accepted Gillingham's offer of £25,000 for the player. Tom Williams, a midfielder, and Danny Jackman, a defender, also joined the club, having last played for Barnsley and Stockport County respectively. Gillingham played pre-season friendly matches against Barnet and Millwall; both Bullock and Williams were injured during these matches and missed the start of the league season. Previewing the new League One season, the view of BBC Sport was that Cooper was faced with "an enormous rebuilding task" and that "consolidating in League One may be the most Gillingham fans could dare to hope for." The team's first-choice kit was blue with white trim; the second-choice kit, to be worn in those away games where there was a clash of colours with the home team, was white with blue trim.

Football League One August–December

Gillingham began the season with a match at their home ground, Priestfield Stadium, against Colchester United. Jackman was included in the starting line-up and Shields made his debut as a substitute. Colchester took the lead but late goals from Andrew Crofts and Darren Byfield gave Gillingham a 2–1 victory. The team remained unbeaten with draws against Port Vale and Scunthorpe United and a 1–0 victory over AFC Bournemouth. Brent Sancho, a defender who had left Dundee at the end of the previous season, made his debut against Bournemouth. On 27 August, Gillingham played Nottingham Forest at Priestfield; Forest had lost their preceding four games but beat Gillingham 3–1. It was the start of a run of five games for Gillingham which included four defeats. Their final match of August ended in a 1–1 draw with Brentford; Neil Harris, making his debut after joining on loan from Nottingham Forest, scored Gillingham's goal. The team began September with three consecutive defeats in which they scored no goals. The run began when Gillingham lost 3–0 away to Rotherham United on 10 September, all the goals coming in the second half. Three days later, in a game which had been rescheduled due to Crofts, Sancho, and Ian Cox being unavailable on the original date because they were representing their countries in international matches, Gillingham lost by the same score to Barnsley, after which they were booed by their own supporters. The run continued with a 1–0 defeat to Oldham Athletic on 17 September.

After Gillingham twice came from a goal down to secure a 2–2 draw with Tranmere Rovers, they ended their six-game winless run in the league when a goal from Sancho in the final five minutes of the match gave them a 1–0 victory at home to Chesterfield on 27 September. The team's first match of October ended in a 2–1 defeat at Priestfield to Southend United, who had won their previous six games and were in second place in the league table. After a 0–0 draw at home to Yeovil Town on 15 October, Cooper criticised his players in the press, saying "It is all right doing it in training, but you have to have the bottle to come out and play at your ground, especially when things have not been going well". A week later, Gillingham appeared to be heading for another goalless draw but conceded a goal in the final minute of the match and lost 1–0 to Bradford City. In the team's final match of October, Gillingham came from a goal down at half-time to secure a 2–1 victory over Blackpool, but they began November with another defeat, losing 3–1 to Hartlepool United. A 2–0 defeat away to Walsall on 12 November left Gillingham in 22nd place in the league table, a position which if maintained would result in relegation to League Two at the end of the season; three days later Cooper resigned from his position as manager. Paul Scally, the club's chairman, told the press "One or two people need to take a hard look at themselves at this club, as there is no doubt Neale was let down in certain areas." Jepson took over the role, initially on a temporary basis, and told the media that he was confident in his ability to turn the team's results around and keep Gillingham from a second consecutive relegation campaign with the squad of players that he had inherited.

In Jepson's first match in charge, Shields scored his first goal for the team to secure a 1–0 victory over Hartlepool United on 19 November; Byfield made his return to the team in the same game, having been absent for nearly two months due to a knee injury. A week later, Gillingham suffered their heaviest defeat of the season so far, losing 5–0 away to Colchester United. It proved to be the final appearance in the Gillingham goal for Bullock, who had made his delayed debut in October but was replaced by Jason Brown after the severe defeat and was released from his contract in January 2006. Gillingham began December by beating Doncaster Rovers 1–0, and four days later secured a fourth consecutive home league victory when they beat Port Vale 3–0 with one goal from Harris and two from Matt Jarvis. The game marked Andy Hessenthaler's final appearance for Gillingham; he was transferred to Barnet the following month. Hessenthaler had been with the club since 1996, making over 350 appearances and serving as player-manager for much of the club's time in the second tier of English football. Harris scored again a week later to give Gillingham the lead away to AFC Bournemouth but the home team scored two goals, the second in the final minute, to win the match. On 26 December, Gillingham drew 1–1 with Bristol City, and five days later they beat Milton Keynes Dons 3–0 at Priestfield. The result meant that Gillingham were in 17th place out of 24 teams in the League One league table at the end of 2005, having won four out of seven league games since Jepson took over, as many victories as had been achieved in 17 league games during Cooper's time in charge.

January–May

Gillingham began the new year with a goalless draw away to Huddersfield Town, and then lost 1–0 away to Barnsley on 10 January. Byfield, who had not played for over a month, was back in the line-up for the latter match. Four days later, he scored the first goal as Gillingham beat Swindon Town 3–0 at Priestfield. A number of fans were arrested and charged with violent disorder as trouble broke out between supporters of the two teams, who share a rivalry. Byfield was required to serve a suspension for the next match due to the number of yellow cards he had received during the season. With injuries meaning that both Shields and Jarvis were also absent, Jepson again included the teenager Akwasi Fobi-Edusei, who had deputised for Byfield the previous month, in the starting line-up against Oldham Athletic on 21 January. Following the game, which Gillingham lost 2–0, the manager described Fobi-Edusei and fellow youngster Gavin Grant, who came on as a substitute, as "not the finished article yet" but noted that "at this moment in time we have no choice, it's all we've got and we have to use those lads." A week later, Grant scored his first goal for the club in a 1–1 draw with Rotherham United. Tommy Black, a midfielder signed on loan from Crystal Palace of the Championship, made his debut in the match. In their final match of January, Gillingham beat Swansea City 2–1, the first time all season that they had won a match away from home. On 4 February, they took the lead against Chesterfield, who had not been beaten in their previous 14 games, but conceded an equalising goal one minute from the end of the match. Gary Mulligan, a forward signed on loan from Sheffield United of the Championship, made his debut in the game.