In the previous season, Gillingham had qualified for the final of the play-offs for promotion to the Football League Second Division but had been defeated.

After a heavy loss to Aldershot in the last game of 1987, manager Keith Peacock was dismissed from his job and replaced by his former assistant Paul Taylor, a decision which was extremely unpopular with the club's supporters.

The highest attendance recorded at the club's home ground, Priestfield Stadium, was 9,267 for an FA Cup match against Birmingham City.

[1] In the 1986–87 season, Gillingham had finished fifth, qualifying for the newly introduced play-offs for the third promotion place, but lost to Swindon Town in the final.

The two teams drew 2–2 on aggregate, necessitating a replay at a neutral venue, which Swindon won 2–0 to ensure that Gillingham would again be playing in the Third Division the following season.

[5][7] Bill Collins, who had been with the club in a variety of roles since the early 1960s,[8] held the post of first-team trainer, and John Gorman managed the youth team.

[10][11] Following Gillingham's failure to win promotion, Tony Cascarino, the previous season's top goalscorer, joined Millwall of the Second Division for a transfer fee of £225,000.

[12][13] Despite having lost the highest-scoring player of the previous season, the club did not immediately sign any new forwards; the only two players to join the club ahead of the new season were George Shipley, a midfielder signed from Charlton Athletic for £40,000, and Gary West, a defender who arrived from Lincoln City for £50,000.

[14] The Gillingham team prepared for the new season with several friendly matches and the club also staged an open day, when supporters could attend autograph sessions with players and watch them training.

After a second consecutive league match in which the team failed to score a goal, a 2–0 defeat away to Grimsby Town, Gillingham defeated Southend United 8–1 on 29 August, the most goals scored by Gillingham in a single match in the Football League since a 9–4 victory over Exeter City in 1951.

[22] Seven days later, Gillingham played Chesterfield, who were joint top of the league table going into the game and had the best defensive record in the division, having not conceded any goals in the first four matches of the season.

[29] Victory over York City on 19 September left Gillingham second in the table,[30] but one draw and two defeats in the next three games meant that the team dropped to twelfth.

[34] Gavin Peacock, son of the manager, also made his debut against Bristol Rovers, having joined the club on a one-month loan from Queens Park Rangers.

The home fans staged a protest against the dismissal of Peacock, who was in attendance at the game; after the match some supporters caught up with the former manager in the car park and carried him on their shoulders down the road outside the stadium.

[34] On 26 March, Gillingham ended their run of winless games by defeating league leaders Notts County away from home.

[55] The team next defeated Preston 4–0, their biggest victory since September, but the attendance of 2,721 was the lowest of the season for a league game at Priestfield.

With his team-mates adopting a defensive strategy, Haylock conceded no goals during the remainder of the game; with the scores still level, a penalty shoot-out was required.

Gillingham lost 3–1 to Aldershot in their first match and drew 2–2 with Leyton Orient in the second and finished bottom of the group, which meant that they failed to qualify for the next round.

Of these, Ian Docker, Ivan Haines and Lee Palmer would all go on to become regulars in the first team, but Neil Luff's single appearance as a substitute would prove to be the only game of his professional career.

[75][76] FW = Forward, MF = Midfielder, GK = Goalkeeper, DF = Defender Taylor remained manager of Gillingham for the start of the 1988–89 season, but was dismissed in October 1988, after only ten months in the job, following a run of poor results.

[25] Peacock returned to management in the summer of 1989 when he was appointed by Maidstone United after they were promoted into the Fourth Division to become Kent's second Football League club.