Robert Taylor scored 18 goals in 19 games by November, after which he was signed by Manchester City for £1.5 million, a new record fee for Gillingham.

On the last day of the regular season, the team had a chance to gain automatic promotion, but lost and instead had to enter the play-offs.

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.

Gillingham also had their best run to date in the FA Cup, beating two Premier League teams before being knocked out by a third, Chelsea, at the quarter-final stage.

[10] Barry Miller, a defender, also stepped up from non-League football, having last played for Farnborough, and former Port Vale defender Brian McGlinchey also joined the club; both players had been released by their previous clubs at the end of the preceding season but played for Gillingham on a trial basis during pre-season and performed well enough to be offered contracts.

[14] Writing in The Times, Nick Szczepanik did not tip Gillingham for a top-six finish, stating that the team had "missed their chance" following the previous season's play-off final defeat.

A new away kit, to be worn in the event of a clash of colours with the home team, was adopted, with yellow shirts replacing the previous season's black and red stripes.

Manager Taylor was ejected from the technical area by the referee for entering the field of play and arguing with him over an unwritten rule that in such circumstances the player taking the throw-in returns the ball to the opposition.

[25][26] Gillingham gained their first league win of the season at the sixth attempt on 4 September, defeating Oldham Athletic 2–1 after scoring two goals in the first six minutes of the match.

[30] On 9 October, Gillingham achieved their biggest win of the season, defeating Wrexham 5–1 at Priestfield; Robert Taylor scored a hat-trick inside the last half-hour of the game.

[23] That match marked Pulis's first appearance at Priestfield since his dismissal from the role of Gillingham manager, as he was now in charge of Bristol City; he received a standing ovation from the home fans.

[23][34] Despite losing their most prolific goalscorer, the team won their first three games without Taylor and were in fifth position in the league table after a 2–1 victory over Colchester United on 26 December.

[28] Gillingham signed two new players on 2 January, making them the first club in English professional football to conclude transfer business in the year 2000.

[36] Striker Iffy Onuora and midfielder Ty Gooden both joined from Swindon Town for a combined transfer fee of £200,000.

[36][37] It marked the start of a second spell at the club for Onuora, who had played for Gillingham between 1996 and 1998;[38] he was a regular starter for the remainder of the season, with Rowe largely used only as a substitute.

[39] The team's first match of 2000 resulted in a 2–2 draw at home to Reading; Thomson gave Gillingham the lead in the 90th minute, but their opponents then equalised in injury time.

[23] It was the start of a run of four consecutive victories, which also included a win away to Preston North End, who had been top of the division going into the match.

[23][41][42] In the match against Preston, striker Carl Asaba, the team's top goalscorer in the previous season, made his first Football League appearance for nine months following a lengthy absence due to a hernia which required three operations.

[44] Gillingham lost consecutive away games against Colchester United and Wycombe Wanderers over the Easter weekend, but then beat Chesterfield 1–0, beginning an eight-game unbeaten run.

[23] This run included victories within four days over two of the other teams chasing promotion, Wigan Athletic and Burnley;[45][46] following the latter win, Stephen Wood of The Times noted that Gillingham were "entering their best form at the perfect moment".

[58] The match at Cheltenham's Whaddon Road ground ended 1–1, necessitating a replay at Priestfield, which Gillingham won 3–2.

[62] The replay also finished 1–1, but unlike in the initial match the rules of the competition meant that extra time was played and Gillingham scored again to win 2–1.

Southall added a third goal in the last 10 minutes and Gillingham won 3–1 to reach the quarter-finals of the FA Cup for the first time.

[28] When his loan ended, he returned to West Ham and played briefly as a substitute in their League Cup quarter-final victory over Aston Villa in December.

Due to the presence on the pitch of an ineligible player, the teams were ordered to replay the match and West Ham lost the second game and were eliminated from the competition.

With several regular players rested, Gillingham were defeated 3–0 by their lower-division opponents and were thus eliminated from the competition at the earliest stage.