The 1938–39 season was Colchester United's second season in their history and their second in the Southern League. Alongside competing in the Southern League, the club also participated in the Southern League Mid-Week Section and Southern League Cup. Colchester won the Southern League title after beating local rivals Chelmsford City to the top of the league by one point. They also reached the 1st round of the FA Cup, where they were eliminated by Folkestone, and finished as runners-up to Tunbridge Wells Rangers in the Mid-Week Section. They reached the semi-final of the Southern League Cup, but the competition could not be completed due to fixture congestion.