The 2006–07 season was Colchester United's 65th season in their history and their first-ever season in the second tier of English football, the Championship. Alongside competing in the Championship, the club also participated in the FA Cup and League Cup. Colchester for the first time ever entered the FA Cup at the third round stage, but were immediately eliminated by League Two Barnet. They suffered a similar fate in the League Cup when another League Two club Milton Keynes Dons knocked the U's out of the competition in extra time.