It was Gillingham's second consecutive season in the second tier of the English football league system, to which the club had gained promotion for the first time in 2000.

[1] In the 1999–2000 season, Gillingham beat Wigan Athletic in the Second Division play-off final to reach the second tier of the English football league system for the first time in the club's history.

[8] Gillingham made only one new signing ahead of the new season: David Perpetuini, a midfielder, joined from Watford just two days before the first game of the campaign, for a transfer fee reported as £100,000.

[9][10] Three players left, including Nicky Southall, who was transferred to Bolton Wanderers of the FA Premier League.

[13] The club announced a new sponsorship deal prior to the season, its most lucrative to date, with the ferry operator SeaFrance, as a result of which the company's name was displayed on the players' shirts.

[23] Following a goalless draw away to Sheffield United, Gillingham won 3–0 at home to Barnsley, King scoring twice in his first start of the season.

[26][27] On 14 September, the team lost 5–1 away to Bradford City, the first time Gillingham had conceded as many goals in a league game since December 1998.

[30] The team's losing run in the league ended on 22 September with a 2–1 victory at home to Rotherham United, and they followed this with an identical result away to Grimsby Town; Chris Hope and King scored Gillingham's goals in both games.

[37] The team's losing streak continued with a 3–1 defeat away to Wimbledon on 20 October and a 2–1 loss away to Birmingham City three days later which left Gillingham in 20th place in the league table.

[17][38] Jlloyd Samuel, a young defender, joined Gillingham on loan from Aston Villa of the Premier League and went straight into the starting line-up for the home game with Walsall on 27 October, replacing the injured Adrian Pennock.

Shaun Goater scored a hat-trick for the home team in a 4–1 victory; BBC Sport described City's performance as "90 minutes of utter domination" and said that they "found little opposition from Gillingham".

[46] Gillingham extended their winning run to three games with a 2–0 victory away to Stockport County on 27 November with goals from Iffy Onoura and King.

[54] It was the final match of Taylor's loan spell; in contrast to his first stint with the club he had failed to score a single goal.

[66] Rick Broadbent of The Times wrote that Gillingham were "no threat" to their opponents, whom Hessenthaler predicted would go on to win the championship of the division.

[67] On 5 March, 19-year-old Jason Brown made his debut for the club, replacing Vince Bartram as starting goalkeeper.

[35] Four days later, the team drew 0–0 with Sheffield Wednesday, who were 20th in the league table going into the game;[71] Richard Copeman of The Sunday Telegraph wrote that Brown "was in superb form".

[76] Hessenthaler described the goal as a "bit of quality" and told the press "I thought we edged it, and we've gone past the 55 points we got last year – a fantastic achievement on fifty grand", referring to, but apparently misquoting, the small amount the club had spent in transfer fees to sign new players since the previous season.

[89] Gillingham's opponents in the fifth round were Arsenal, who in the previous season had been beaten finalists in the FA Cup and finished second in the Premier League.

[90] With a higher-priority UEFA Champions League match upcoming, Arsenal made a number of changes to their team for the game.

[93] Twice Arsenal took the lead only for Gillingham to equalise, the second time with a lobbed goal from Ty Gooden which BBC Sport described as "sensational" and "stunning".

[94] Both Henry and Pires were then brought on, which Clive White of The Sunday Telegraph said was done "out of respect for the opposition",[91] after which Arsenal scored three more goals to secure a 5–2 victory which BBC Sport said made the match look more one-sided than it had actually been.

[98] Gillingham conceded a goal in the first half and were losing until eight minutes from the end of the game when King scored from a penalty kick.

[103] Southampton had a number of further goalscoring chances in the second half but did not score again until the 83rd minute when they made it 2–0, which proved to be the final result, meaning that Gillingham were eliminated from the competition.

[51] FW = Forward, MF = Midfielder, GK = Goalkeeper, DF = Defender Less than three weeks after the season ended, King was sentenced to 18 months in prison after being caught driving a stolen car the previous year.

In the 2003–04 season, they finished 21st, level on points with 22nd-placed Walsall, and avoided relegation only by virtue of a superior goal difference.