The 1965–66 season was Colchester United's 24th season in their history and their first back in the fourth tier of English football, the Fourth Division, following relegation the previous season. Alongside competing in the Fourth Division, the club also participated in the FA Cup and the League Cup. Colchester were immediately promoted back to the Third Division after ending the season in fourth position. Queens Park Rangers handed Colchester another early FA Cup exit following a replay, while Middlesbrough knocked the U's out of the League Cup in the second round.