The team struggled in August and September, and did not win a Third Division match until the eighth league game of the season.

Gillingham's form remained inconsistent and, although they climbed to 10th in the 22-team league table in October, the team spent most of the season in the bottom half and finished 16th.

[4][5] Watford were later fined £10,000 (equivalent to £30,000 in 2023) by the Football Association, the governing body of the sport in England, for making an illegal approach to Roeder.

[13] The away kit, to be worn in the event of a clash of colours with the home team, was all red with similar black and white panels on the shirts.

Alan Gough, a goalkeeper who had recently left Fulham, played on a trial basis against Charlton but Gillingham opted not to sign him to a contract.

Both Smillie and Micklewhite made their debuts in a game which finished 2–0 to Gillingham's opponents;[15][16] a week later the team again lost without scoring a goal, losing 3–0 away to Rochdale.

[18] After a late goal from Nicky Forster gave the team a third consecutive league draw against Wycombe Wanderers, Flanagan told the press that "the sign of a good side is that they can roll their sleeves up and battle back.

[21] The team won their first league game of the season at the eighth attempt, defeating Scunthorpe United 1–0 on 25 September with a goal from Smillie.

[16] Gillingham ended their losing run in the final game of 1993 on 27 December, beating Northampton Town 1–0 at home with an own goal from Steve Terry; the attendance of 4,573 was the largest recorded at Priestfield during the season.

[31] The start of the match was delayed by 40 minutes as an electricity board worker had to be called out to disengage a timer switch which prevented the floodlights being turned on on weekday afternoons.

[34] Gillingham began 1994 with a second consecutive 1–0 win at Priestfield, defeating Bury with a goal from Smillie on 1 January;[17] the result took the team back up to 14th in the table.

[17] Gillingham ended their winless run with a 1–0 win away to Torquay United on 5 March, but lost again seven days later away to Shrewsbury Town.

As a Third Division team, Gillingham entered the 1993–94 FA Cup in the first round and were drawn to play away to Yeading of the Isthmian League Premier Division, two levels lower in the English football league system, who had progressed through four qualifying rounds to reach this stage of the competition for the first time.

^ The match was played at Hayes's Church Road ground, but remained officially a home game for Yeading rather than being considered to have taken place at a neutral venue.

The first leg of the two-legged tie took place at Priestfield and Gillingham defeated their higher-level opponents 1–0 with a goal from Robbie Reinelt.

[53] Eight days later, however, Brighton won the second leg at the Goldstone Ground 2–0 and eliminated Gillingham from the competition by an aggregate score of 2–1.

Gillingham's first group match was at home to Colchester in late September and resulted in a 0–0 draw;[56] the attendance of 1,091 was the lowest recorded at Priestfield during the season.

[31] FW = Forward, MF = Midfielder, GK = Goalkeeper, DF = Defender Eight days after the last game of the season, the club staged a gala centenary match at Priestfield featuring two teams of past and present Gillingham players managed by former Gillingham player Ernie Morgan and former manager Keith Peacock.

In January 1995, after several seasons spent near the bottom of the Football League coupled with nearly a decade of financial difficulties, the club was declared insolvent and placed in receivership.