Prior to the new season, Gillingham signed seven new players, paying a new club record transfer fee for Watford's Andy Hessenthaler.

The team's form was poor in the first half of the season and at the end of 1996, Gillingham were in 21st position in the 24-team league table, putting them in danger of relegation back to the fourth tier.

Iffy Onuora, who joined the club at the start of the season, was top goalscorer, with 21 goals in the Second Division and a total of 23 across all competitions.

The highest attendance recorded at the club's home ground, Priestfield Stadium, was 10,603, for the League Cup match against Coventry City.

A number of players who had been regulars at the lower level departed, including Dave Martin, captain of the promotion-winning team.

The highest fee other than that paid for Hessenthaler was £65,000 (equivalent to £150,000 in 2023) for Lenny Piper, a teenaged midfielder who joined the club from Wimbledon.

[12] Two further players, both defenders, arrived on free transfers: Ian Chapman from Brighton & Hove Albion and John Humphrey from Charlton Athletic.

New signings Bryant, Ford, Humphrey, Hessenthaler, Chapman and Onuora were all in the starting line-up, and Piper came on as a substitute to score the winning goal in the final minute to give his team a 3–2 victory.

[17] In the next game, Onuora achieved the team's only hat-trick of the season, scoring all three goals in a 3–1 victory at home to Rotherham United.

[21] Gillingham ended the winless run with a victory over Peterborough United on 19 November, despite goalkeeper Jim Stannard suffering an injury and defender Mark Harris having to take over in goal.

[26] Gillingham's final match of 1996 was away to Burnley, who won 5–1; Onuora was sent off after receiving a second yellow card for angrily throwing the ball at the assistant referee.

[29][30] Due to the postponement of a number of scheduled matches, the first league game of 1997 did not take place until 18 January and resulted in a 1–1 draw with Notts County.

[34] In March, Fortune-West was fit again after his injury but could not regain a place in the team due to the form of Onuora and Akinbiyi and was sent on loan to Leyton Orient of the Third Division.

[35][36] Beginning with the game against Wycombe Wanderers on 22 March, Onuora scored in five consecutive matches, making him only the seventh player to achieve this feat for Gillingham in the Football League.

[43] The teams from the top two divisions of English football entered the competition in the third round and Gillingham were paired with Derby County of the FA Premier League.

The game took place on 14 January and by the midway point of the second half remained goalless, however the referee abandoned the match due to the frozen pitch.

[44][45] The game was rescheduled for a week later; with forwards Onuora, Akinbiyi and Bailey all unavailable due to injury or suspension, Gillingham played poorly and lost 2–0.

[53][54] The replay took place at Coventry's Highfield Road ground, and a second half goal from Neil Smith gave Gillingham a 1–0 win; Trevor Haylett of The Guardian attributed Gillingham's victory to their "compact, disciplined rearguard in which their three centre-halves stood tall all night against a Coventry attack whose ideas petered out after a bright opening spell".

A goal approximately 15 minutes from the end of the game gave Ipswich a 1–0 win and Gillingham, for whom Ratcliffe was sent off, were eliminated from the League Cup.

[58][59] Bryant was missing from the Gillingham team and Pulis admitted after the match that this was because the defender had been accidentally shot in the leg while participating in field sports.