The 1960–61 season was Colchester United's 19th season in their history and their eleventh season in the third tier of English football, the Third Division. Alongside competing in the Third Division, the club also participated in the FA Cup and the new League Cup competition. Colchester reached the second round in both cups, beating Maidenhead United in the first round of the FA Cup before being eliminated by Aldershot. In the League Cup, Colchester hosted First Division Newcastle United in the first round. They won 4–1, but were knocked out by Southampton in round two.