| 30. Round | 26/01/2013 | Colchester United | - | Walsall FC | 2:0 | ||||
| 31. Round | 02/02/2013 | Portsmouth FC | - | Colchester United | 2:3 | ||||
| 25. Round | 05/02/2013 | Colchester United | - | Swindon Town | 0:1 | ||||
| 32. Round | 09/02/2013 | Colchester United | - | Preston North End | 1:0 | ||||
| 33. Round | 16/02/2013 | Sheffield United | - | Colchester United | 3:0 | ||||
| 34. Round | 23/02/2013 | Colchester United | - | Tranmere Rovers | 1:5 | ||||
| 37. Round | 09/03/2013 | Colchester United | - | Crewe Alexandra | 1:2 | ||||
| 39. Round | 16/03/2013 | Bury FC | - | Colchester United | 1:2 | ||||
| 42. Round | 01/04/2013 | Oldham Athletic | - | Colchester United | 1:1 | ||||
| 43. Round | 06/04/2013 | Colchester United | - | Leyton Orient | 2:1 | ||||
| 44. Round | 13/04/2013 | Notts County | - | Colchester United | 3:1 | ||||
| 46. Round | 27/04/2013 | Carlisle United | - | Colchester United | 0:2 |
England