Gillingham's results in the first half of the season were poor, including a 9–2 defeat to Nottingham Forest, the highest number of goals the team had conceded for more than 20 years; at the end of 1950 they were second bottom of the Third Division South league table.

In January and early February Gillingham climbed to 19th in the 24-team division after winning five times in six games, including a 9–4 victory over Exeter City, a new record for the club's highest Football League score which would stand for more than 30 years.

Dave Thomas, who joined the club in October, finished the season as the team's top goalscorer; he scored 19 times in the Football League and twice in the FA Cup.

Larry Gage, a goalkeeper, Randolph Jenkins, an inside forward, Harry Ayres, a half-back, and Ron Lewin, a full-back, all joined from Fulham for a combined transfer fee of £14,000 (equivalent to £605,900 in 2023).

[19][20] Gillingham's first match of the season was at home to the other newly elected club in the division, Colchester United; new signings Gage, Lewin, Ayres and Veck all made their debuts.

A correspondent for the Western Daily Press complimented Gage on his goalkeeping against Bristol Rovers, writing that Gillingham's opponents should have scored at least six goals as opposed to the three which they did.

They ended September with defeats against Leyton Orient and Ipswich Town, both without scoring a goal, and then began October by losing away to Crystal Palace.

[21] A week later, Dave Thomas, a centre-forward newly signed from Watford,[32] made his debut in a 1–1 draw with Brighton & Hove Albion.

[21] Gillingham began November with a 4–1 defeat away to Northampton Town,[21] after which they were 21st in the Third Division South table, one point above the three teams tied for last place.

[38][39] Despite having only joined the club in October, Thomas was the team's leading Football League scorer, with eight goals in twelve games.

[21] On 17 February, they lost 5–1 away to Ipswich Town;[48] a week later they drew 0–0 with Crystal Palace but forward Charlie Burtenshaw suffered a broken leg which kept him out of the team for over a year.

[52][53] Gillingham began April with a third consecutive defeat, losing 4–1 at home to Nottingham Forest, for whom Wally Ardron scored a hat-trick before half-time.

[54] Veteran goalkeeper Johnny Burke, a regular starter for Gillingham in the Southern League, replaced Gage for the next game, a 2–1 victory away to Torquay United.

[21][59] Gillingham ended the season with a 2–1 defeat at home to Plymouth Argyle,[60] leaving them 22nd in the Third Division South, six points above the bottom two teams, who were required to apply for re-election to the Football League.

As a Third Division South club, Gillingham entered the 1950–51 FA Cup in the first round; their opponents were Linby Colliery of the Central Alliance, a semi-professional team including several players employed at the eponymous mining facility.

Thomas gave Gillingham the lead before Rovers scored twice; a late goal from Jackie Carr meant that the game ended in a draw and a replay was required.

[21] FW = Forward, HB = Half-back, GK = Goalkeeper, FB = Full-back Gillingham's first season back in the Football League was not a success in financial terms; transfer fees and increased wages meant that the club registered a loss of £12,483 (equivalent to £495,300 in 2023).

[55] Veck, the team's second-highest goalscorer, was offered a new contract with the club but rejected it and signed for Chelmsford City of the Southern League.