The team started the season strongly and by the end of October were challenging for promotion, but then went on a lengthy run of games without a win which saw them slip into the bottom third of the league table in December.

Results improved in the second half of the season, and Gillingham were sixth in the table with one game remaining, which would be sufficient for a place in the promotion play-offs.

Foods of Sevenoaks signed a contract to become the club's new primary sponsor, meaning that their Kool brand appeared on the players' shirts.

[12] Gillingham prepared for the new season with a number of friendly matches, including games against Crystal Palace and Queens Park Rangers.

After being forced to leave the Goldstone Ground due to financial difficulties, Third Division Brighton & Hove Albion signed a two-year agreement to groundshare with Gillingham.

[14] Their opening home game on 16 August against Macclesfield Town was the first Football League match to take place at Priestfield without involving Gillingham.

[15] Gillingham's first Second Division game of the season was at home to Preston North End on 9 August; Ashby, Moss, Smith, and Masters all made their debuts.

[16] With the previous season's top goalscorer, Iffy Onoura, missing following a knee operation,[17] Steve Butler was chosen to partner Ade Akinbiyi in the forward positions.

[16] Gillingham lost both the last game of August and the first of September, after which they were 15th out of 24 teams in the league table,[22] but wins at home to AFC Bournemouth and away to Bristol Rovers took them up to 9th.

[25] The victories meant that by the end of the month, Gillingham had climbed to fourth in the table, only two points off the two automatic promotion places.

[16] Defender Mark Patterson, a £45,000 (equivalent to £100,000 in 2023) signing from Plymouth Argyle, made his debut in a 3–1 defeat to Millwall on 1 November, during which Statham was sent off.

[38][27] Gillingham's final match of 1997 was at home to Brentford on 29 December; Akinbiyi scored twice in a 3–1 victory, the team's first win in more than two months.

[42][43] Akinbiyi scored both goals, one in each half;[44] goalkeeper Mark Walton, signed on loan from Fulham, made his debut.

[45] The transfer was initially processed as a loan due to a technicality and he was set to sign a permanent contract with Gillingham after the match against Watford, but the club refused to meet his salary request and he instead returned to Fulham.

[46] Victory over Oldham Athletic on 3 March took Gillingham up to 6th in the table, putting them within the promotion play-off places,[27][47] but they lost the next game 1–0 to Millwall and defender Guy Butters suffered a broken leg which would keep him out of the team for the rest of the season.

[18] The result, along with those of the day's other games, left Gillingham in a four-way tie with Bristol Rovers, Fulham, and Wrexham on 70 points; under Football League tiebreaker rules the teams were ranked in order of the total number of goals each had scored.

[27][55] A shot by Southall struck the goalpost and rebounded away in the final minute of the game against Wigan; had he scored and his team held onto their lead for the remaining seconds, they would have qualified for the play-offs.

[73] Gillingham were 2–0 up with less than ten minutes remaining but conceded two late goals, and Manchester City won the subsequent penalty shoot-out to gain promotion.