| 1. Round | 05/08/2006 | Birmingham City | - | Colchester United | 2:1 | ||||
| 5. Round | 26/08/2006 | Colchester United | - | Derby County | 4:3 | ||||
| 6. Round | 09/09/2006 | Burnley FC | - | Colchester United | 1:2 | ||||
| 9. Round | 23/09/2006 | Leicester City | - | Colchester United | 0:0 | ||||
| 12. Round | 18/10/2006 | Colchester United | - | Sheffield Wednesday | 4:0 | ||||
| 17. Round | 11/11/2006 | Leeds United | - | Colchester United | 3:0 | ||||
| 29. Round | 20/01/2007 | Ipswich Town | - | Colchester United | 3:2 | ||||
| 30. Round | 30/01/2007 | Colchester United | - | Preston North End | 1:0 | ||||
| 31. Round | 03/02/2007 | Colchester United | - | Birmingham City | 1:1 | ||||
| 32. Round | 10/02/2007 | Barnsley FC | - | Colchester United | 0:3 | ||||
| 33. Round | 13/02/2007 | Colchester United | - | West Bromwich Albion | 1:2 | ||||
| 34. Round | 20/02/2007 | Plymouth Argyle | - | Colchester United | 3:0 | ||||
| 36. Round | 02/03/2007 | Derby County | - | Colchester United | 5:1 | ||||
| 39. Round | 16/03/2007 | Southampton FC | - | Colchester United | 1:2 | ||||
| 41. Round | 06/04/2007 | Southend United | - | Colchester United | 0:3 | ||||
| 46. Round | 06/05/2007 | Colchester United | - | Crystal Palace | 0:2 |
England