Gillingham's form was inconsistent in the first half of the season; after falling to 17th in the league table, the team began a lengthy unbeaten run and were 10th at the end of 1990.

Around the end of March, Peter Beadle and David Crown, two of the team's regular starting forwards, were injured and both missed most of the remainder of the season.

The highest attendance recorded at the club's home ground, Priestfield Stadium, was 8,004, for a game against local rivals Maidstone United.

[5] Richardson signed only one new player ahead of the new season: David Crown, a 32-year old forward who had played nearly 400 Football League games and scored over 120 goals, joined from Southend United for a transfer fee of £50,000 (equivalent to £140,000 in 2023).

[6][7] Veteran defender Paul Haylock was among several players released by the club; after playing nearly 200 games for Gillingham he joined their local rivals Maidstone United.

[14] On 15 September, Hillyard made his final appearance for Gillingham in a 2–1 defeat away to Scarborough, injuries bringing an end to a playing career with the club which had begun in 1974.

[24][25] Three days later, David McDonald, a teenaged defender signed on loan from Tottenham Hotspur of the Football League First Division after an injury to Joe Dunne, made his debut in a 1–1 draw against York City;[26] Ian Docker scored his first goal for Gillingham after more than 50 games for the team.

[14][30] On 9 November Gillingham won for the first time in five weeks with a 2–1 victory over Halifax Town; Crown scored the opening goal, his first for the club.

[14][32][33] The team's final game of 1990 was a goalless draw at home to Northampton Town; Gillingham ended the year 10th in the Fourth Division, three points below the promotion play-off places.

[34][35] Gillingham's first match of the new year ended in a 1–1 draw away to Stockport County on 1 January with a goal from 18-year-old forward Peter Beadle,[36] who had played intermittently in the first half of the season, mainly as a substitute.

[20] As this resulted in Lim serving a three-match suspension, Richardson signed goalkeeper Peter Gleasure on loan from Northampton Town to cover his absence.

[40] Paul Hague, a teenaged defender, made his debut away to Carlisle United on 12 March,[41] a game which Gillingham won 4–0, the team's biggest away win since 1968.

[15] Crown's replacement against Lincoln was Adrian Owers, a midfielder newly signed on loan from Brighton & Hove Albion for the remainder of the season.

[48] Tony Butler, another teenaged defender, made his debut in a 2–2 draw against Blackpool on 20 April and retained his place in the team for the remainder of the season; he went on to play 180 games for the club.

[25] Gillingham's winless run extended to ten games with three defeats in which they failed to score any goals, culminating on 4 May with a 3–0 loss away to Wrexham,[14] who were bottom of the division.

[52] The run finally ended in the last match of the season at home to Doncaster Rovers when goals from Mark O'Connor and Lovell gave Gillingham a 2–0 victory.

[59] Three weeks later Gillingham defeated Maidstone 4–1 at home; the result meant that they finished second in the group and qualified for the first round proper, in which their opponents were fellow Fourth Division team Hereford United.

[63] Gary West, who had a brief loan spell with the club,[64] and teenagers Dave Jordan and Mark Dempsey, who both made their professional debut during the season, tied for the fewest games played, each making only 2 appearances.

FW = Forward, MF = Midfielder, GK = Goalkeeper, DF = Defender Writing in the programme for the final match of the season, the club's chief executive, Barry Bright, expressed "abject disappointment" at the team's failure to achieve promotion, blaming injuries to key players and the fact that too many games resulted in draws.