In the second half of the season the team's form remained inconsistent: they lost every league game in January but had a six-game unbeaten run in March and April.

John Boden, Dick Goffin, and Charlie Hafekost were the joint highest scorers in league matches only, with five goals each.

The highest attendance recorded at the club's home ground, Priestfield Road, was 11,321 for the FA Cup match against Barnsley.

[9] New players to join the club included Arthur Wolstenholme, a forward who had last played for Blackpool of the Football League Second Division.

[14][16] Gillingham achieved their first win of the season on 21 September when a late goal from Albert Court gave them a 1–0 victory away to Brentford.

[14][18] The game on 12 October against Swindon Town ended in a third consecutive home 0–0 draw; the first goal of the season at Priestfield Road was scored four days later by Reading, who went on to secure a 4–0 victory.

[14][23] The team ended a six-match winless run with a 2–1 victory away to Coventry City on 16 November with goals from John Boden and Dick Goffin.

[14][24] A week later, Boden scored Gillingham's first goal of the season at Priestfield Road in their seventh home game.

[34] Gillingham again failed to score in the next league game, losing 4–0 at home to Brentford; it was the first time Brentford had won away from home during the season and the writer for the Daily Herald commented that the Gillingham players looked tired after playing an FA Cup game two days earlier.

[35][36] Bailey returned to the team on 25 January for the first time since October; a 2–1 defeat away to Millwall meant that Gillingham had lost every league game during the month.

[14] Despite the new-look line-up, the writer for The People noted that the Gillingham forwards "worked neatly together in the early stages and gave the visitors' defenders great anxiety".

[14] Following two draws, a goal from Church gave Gillingham a 1–0 win away to Crystal Palace on 12 April,[48] extending the team's unbeaten run to six games.

[52] John and Lee gave Gillingham a half-time lead and Johnson scored two goals after the interval, both from penalty kicks.

As a Southern League Division One team, Gillingham entered the 1912–13 FA Cup at the fourth qualifying round stage; they were due to play Leyton on 1 December but received a walkover as their opponents withdrew from the competition.

[14] Gillingham had a number of goalscoring chances against the reigning cup-holders but were unable to convert them and the game ended in a goalless draw.

[14] FW = Forward, HB = Half-back, GK = Goalkeeper, FB = Full-back Prior to the next season, Gillingham opted to employ a full-time team manager, appointing the former Liverpool player Sam Gilligan as player-manager.

[61] In the 2012–13 season Gillingham wore a modern version of the red and blue shirts to mark the centenary of the club changing its name.