Gillingham were 2–0 up with less than ten minutes remaining but conceded two late goals, and Manchester City won the subsequent penalty shoot-out to gain promotion.

Despite leading the team to the play-off final, manager Tony Pulis was dismissed from his job shortly afterwards amid allegations of gross misconduct.

[3] Tony Pulis served as manager for a fourth season, having been appointed in 1995 after chairman Paul Scally purchased the club.

[6] There were significant changes to the playing squad ahead of the season, and the records for the highest transfer fees received and paid by Gillingham were both broken.

Shortly after the end of the 1997–98 season, Jimmy Corbett, an attacking midfielder who had debuted in August 1997 at the age of 17, moved to FA Premier League club Blackburn Rovers for an initial fee of £525,000 (equivalent to £1.27 million in 2023); clauses in the contract meant that the fee had the potential to nearly double if Corbett played more than a specified number of games at the higher level.

[18][19] Gillingham achieved their first victory of the season at the fifth attempt, defeating Wrexham 4–0; Asaba scored his first goal since joining the club and the result took the team up to 12th in the table.

[22][23] The following game, a 2–2 draw at home to Macclesfield Town, was preceded by the arrival by helicopter of the club's new mascot, Tommy T.

[24] Between 20 October and 10 November, Asaba scored in five consecutive games, four of which resulted in victories, taking his total number of league goals to ten.

[25] Taylor, however, had only scored three league goals and was receiving negative reactions from some Gillingham supporters, who considered him out of shape and his large transfer fee a waste of money.

[25] Gillingham ended 1998 with a 1–1 draw at home to Millwall in front of 9,221 fans, the season's largest attendance at Priestfield Stadium to date.

Two weeks later, however, the red card was overturned by a special commission convened by the Football Association, the sport's governing body in England, based on evidence provided by police officers present at the game.

[33] In the final game of February, Gillingham recorded their best ever Football League win away from home when they beat Burnley 5–0 at Turf Moor; Taylor scored all five goals.

[36] In the following match, Taylor scored in the final minute to gain the team a draw against fellow promotion contenders Preston North End.

[37][38] In March, Gillingham lost 4–1 to Wigan Athletic, the most goals conceded by the team in a single game during the season, but followed it up with a 4–0 win over Lincoln City.

[39] Gillingham began the month of April with three consecutive victories; this included a win at home to Bournemouth with goals from Hessenthaler and Lisbie.

Four days after the second of these victories, Wigan Athletic lost to Wycombe Wanderers, meaning that Gillingham were guaranteed a place in the play-offs irrespective of the result of the final match of the regular season.

[45] Gillingham's final game resulted in a 1–0 win away against Notts County, Asaba scoring the only goal; this meant that they finished the regular season fourth in the table, seven points below second place.

[49] Having been largely thwarted by the Gillingham defence in the open 45 minutes, Preston had more goalscoring chances in the second half; goalkeeper Vince Bartram dived full-length across his goal to keep out a shot from Jon Macken.

In the first round of the 1998–99 Football League Trophy, a competition for Second and Third Division teams, Gillingham played Colchester United.

[58] FW = Forward, MF = Midfielder, GK = Goalkeeper, DF = Defender One month after the play-off final, Pulis was dismissed from his job as the club's manager, amid accusations of gross misconduct on his part,[61] a decision which led to a lengthy and acrimonious court case between him and Scally.

[62][63] The relationship between the two had deteriorated during the 1998–99 season, in particular following an interview with local newspaper Kent Today, which quoted Scally as saying that being a manager was an "easy job".

[68] After defeating Stoke City in the semi-finals, Gillingham beat Wigan Athletic in the final to gain promotion to the second tier of the English football league system for the first time in the club's history.