The 2012–13 season was Colchester United's 71st season in their history and fifth successive season in the third tier of English football, League One. Alongside competing in the League One, the club also participated in the FA Cup, the League Cup and the Football League Trophy. Colchester exited each cup competition after just one game, suffering defeats at Yeovil Town and Northampton Town in the League Cup and League Trophy respectively, while they were humiliated in the FA Cup first round by non-League Essex rivals Chelmsford City by a 3–1 margin.