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. 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.