The 2008–09 season was Colchester United's 67th season in their history and first season back in the third tier of English football following relegation, League One. Alongside competing in League One, the club also participated in the FA Cup, the League Cup and the Football League Trophy. Colchester were eliminated from the FA Cup at the first round stage by Leyton Orient, while rivals Ipswich Town beat the U's at Portman Road in the second round of the League Cup. They made the area semi-final of the Football League Trophy where they lost out to Luton Town.