| 1. Jornada | 09.08.2008 | Hartlepool United | - | Colchester United | 4:2 | ||||
| 3. Jornada | 23.08.2008 | Swindon Town | - | Colchester United | 1:3 |  |
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| 4. Jornada | 30.08.2008 | Colchester United | - | Oldham Athletic | 2:2 | ||||
| 7. Jornada | 20.09.2008 | Colchester United | - | Milton Keynes Dons | 0:3 | ||||
| 11. Jornada | 18.10.2008 | Stockport County | - | Colchester United | 1:2 | ||||
| 12. Jornada | 21.10.2008 | Colchester United | - | Millwall FC | 1:2 | ||||
| 13. Jornada | 25.10.2008 | Colchester United | - | Carlisle United | 5:0 | |
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| 15. Jornada | 01.11.2008 | Southend United | - | Colchester United | 3:3 |  |
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| 16. Jornada | 15.11.2008 | Colchester United | - | Walsall FC | 0:2 | ||||
| 36. Jornada | 07.03.2009 | Oldham Athletic | - | Colchester United | 0:1 | ||||
| 37. Jornada | 10.03.2009 | Colchester United | - | Swindon Town | 3:2 | ||||
| 30. Jornada | 31.03.2009 | Millwall FC | - | Colchester United | 0:1 | ||||
| 42. Jornada | 11.04.2009 | Leyton Orient | - | Colchester United | 2:1 | ||||
| 43. Jornada | 13.04.2009 | Colchester United | - | Brighton & Hove Albion | 0:1 | ||||
| 44. Jornada | 18.04.2009 | Hereford United | - | Colchester United | 0:2 |
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