In late October, after the eighth of these defeats, Paul Taylor was dismissed as the club's manager and replaced by Keith Burkinshaw.

Steve Lovell was the team's top goalscorer for the second consecutive season; he scored 14 goals in Third Division matches and a total of 17 in all competitions.

The highest attendance recorded at the club's home ground, Priestfield Stadium, was 5,871 for a league game against Fulham on 26 December 1988.

[9] Taylor signed one new player ahead of the new season: George Burley, a 32-year-old defender who had played nearly 450 games in the Football League, joined the club from Sunderland.

[12] Gillingham's first game of the season took place at their home ground, Priestfield Stadium, on 27 August against Swansea City, who won 3–2;[13] Burley made his debut, as did Brian Clarke, a teenaged defender from the youth team.

[13] The sequence began with a 2–1 defeat away to Mansfield Town on 20 September and continued with four games in which Gillingham failed to score any goals, losing to Reading, Brentford, Bristol City and Chesterfield,[13] after which the team had fallen to 20th in the table, only one position above the four relegation places.

[18][19] On 25 October, Gillingham lost 5–0 away to Preston North End, the team's eighth consecutive league defeat;[13] the following day Taylor was dismissed from his role as manager by the club's board of directors.

[23] The run of consecutive defeats finally came to an end on 8 November when a goal from Burley gave Gillingham a 1–0 win at home to Blackpool.

[13] Mark Stimson, a young defender signed on loan from Burkinshaw's former club Tottenham Hotspur of the First Division, made his debut against Sheffield United.

[13] After a goalless draw at home to Brentford on 4 February, Gillingham were bottom of the Third Division and remained there at the end of the month.

[30][31] Burkinshaw continued to sign new players; Tim O'Shea, a defender who had joined from Leyton Orient, played for the first time against Brentford.

[37] Gavin also scored in both of the next two games, including a 2–1 win at home to Wigan Athletic on 24 March which gave Gillingham their first victory of 1989.

Barry Bright, the club's chief executive, said that he had received around twenty applications for the managerial position and anticipated drawing up a shortlist of around five, of which Richardson would be one.

[13] Defeat at Blackpool on 1 May meant that Gillingham could no longer overtake the team then in 20th place, confirming that the club would be relegated to the Fourth Division at the end of the season.

[36][43] Gillingham finished 23rd in the league table, 14 points below 20th-placed Northampton Town,[19] and were thus relegated to the Fourth Division, ending a spell of 15 years at the third tier of English football.

[24] Gavin Peacock had the second highest number of appearances, with 52, and four other players played between 40 and 50 times: Dave Smith, Lovell, Ian Docker and Paul Haylock.

Two players made only one appearance: Eamonn Collins, who had a brief loan spell at Gillingham,[56] and Irvin Gernon, who was transferred to Reading early in the season.

[35] FW = Forward, MF = Midfielder, GK = Goalkeeper, DF = Defender Peacock was voted the club's player of the year, but following the team's relegation he was signed by AFC Bournemouth of the Second Division,[59] as was Phil Kite.

After a Football League inquiry, Gavin's move to Leicester was ruled valid, but it was agreed that he should be loaned back to Gillingham for the 1989–90 season.