The 1961–62 season was Colchester United's 20th season in their history and their first-ever season in the fourth tier of English football, the Fourth Division. Alongside competing in the Fourth Division, the club also participated in the FA Cup and the League Cup.

Colchester bounced back to the Third Division at the first time of asking, earning their first promotion in the club's history by finishing as runners-up. By the end of the campaign, Colchester trailed Millwall by just one point, winning 23 games and scoring 104 league goals with Bobby Hunt the division's top scorer. The club experienced their record victory during the season when they beat Bradford City 9–1 on 30 December.

In the cup competitions, first-round exits were experienced in both FA and League cups. Colchester were beaten at home to Crewe Alexandra in September in the League Cup, while it took Peterborough United three attempts to overcome Colchester in the FA Cup first round following a second replay.

At the end of a very disappointing 1960–61 season, manager Benny Fenton cut his playing squad by ten players, with players including Neil Langman, Chic Milligan and Tommy Williams all released. The club was over £3,300 in debt, and so a fresh start required for the new season with a new, slimline squad. Just 17 players would be used in the new campaign, with eight of those playing over 40 of the 44 league games possible.

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