The 1999–2000 season was Colchester United's 58th season in their history and their second successive season in the third tier of English football, the Second Division. Alongside competing in the Second Division, the club also participated in the FA Cup, the League Cup and the Football League Trophy. Colchester suffered first round exits once more in all three cup competitions after Crystal Palace beat the U's 5–3 over two legs in the League Cup, and Swansea City dumped them out of the FA Cup and Football League Trophy.