| 16. Round | 15/11/2008 | Colchester United | - | Walsall FC | 0:2 | ||||
| 35. Round | 03/03/2009 | Huddersfield Town | - | Colchester United | 2:2 | ||||
| 36. Round | 07/03/2009 | Oldham Athletic | - | Colchester United | 0:1 | ||||
| 37. Round | 10/03/2009 | Colchester United | - | Swindon Town | 3:2 | ||||
| 38. Round | 14/03/2009 | Colchester United | - | Crewe Alexandra | 0:1 | ||||
| 39. Round | 21/03/2009 | Leicester City | - | Colchester United | 1:1 | ||||
| 40. Round | 28/03/2009 | Scunthorpe United | - | Colchester United | 3:0 | ||||
| 30. Round | 31/03/2009 | Millwall FC | - | Colchester United | 0:1 | ||||
| 41. Round | 04/04/2009 | Colchester United | - | Leeds United | 0:1 |
England