The 1939–40 season was Colchester United's third season in their history and their third in the Southern League. Alongside competing in the Southern League, the club were also due to participate in the Southern League Mid-Week Section, FA Cup and Southern League Cup. They were also due to play the Southern League Cup matches remaining from the previous season during the campaign, but only played the outstanding semi-final fixture against Norwich City Reserves. The season was to end prematurely, with competitive football abandoned with the outbreak of World War II. Colchester United played regular season fixtures until 2 September 1939, with the 0–0 draw at Layer Road with Ipswich Town Reserves the final competitive fixture to be played by the club for almost six years.