The 1949–50 season was Colchester United's eighth season in their history and their eighth and final season in the Southern League. Alongside competing in the Southern League, the club also participated in the FA Cup and Southern League Cup. The club finished as runner-up to Merthyr Tydfil in the league, but despite this Colchester were elected to the Football League at the end of the campaign with the expansion of the League from 88 to 92 clubs. The club won the Southern League Cup 6–4 on aggregate, while they exited the FA Cup at the fourth qualifying round stage following a 1–0 defeat by Wealdstone.

Layer Road suffered storm damage ahead of the 1949–50 season, and owing to a shortage of steel, re-construction work was not complete as the season commenced. Manager Jimmy Allen strengthened his defence with the signing of Reg Stewart from Sheffield Wednesday and Bill Layton from Bradford Park Avenue, and by Christmas 1949, Colchester had lost just three of their 28 games played, one of which was the 1–0 FA Cup fourth qualifying round defeat to Wealdstone. The game was one of the first FA Cup ties to be broadcast on television, but on this occasion it was the U's who were on the receiving end of a cup shock.

Colchester had topped the table all season until a fixture-congested April, which saw them held to home draws by Torquay United Reserves and Gravesend & Northfleet, while suffering 5–0 and 6–1 defeats at main title rivals Merthyr Tydfil and Gillingham in the space of three days. Between those defeats, the U's had recovered some pride with a 3–0 Southern League Cup final first-leg win over Bath City. Competing in their fourth match in just five days, a weary Colchester side allowed Bath to lead the second-leg 4–1, meaning the tie would go to extra time. Vic Keeble and Dennis Hillman scored in the added 30-minutes, helping Colchester lift the trophy for the second time.

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