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.