| 1. Round | 09/08/2008 | Leyton Orient | - | Hereford United | 2:1 | ||||
| 2. Round | 16/08/2008 | Peterborough United | - | Leyton Orient | 3:0 | ||||
| 3. Round | 23/08/2008 | Leyton Orient | - | Carlisle United | 0:0 | ||||
| 4. Round | 30/08/2008 | Brighton & Hove Albion | - | Leyton Orient | 0:0 | ||||
| 5. Round | 06/09/2008 | Walsall FC | - | Leyton Orient | 0:2 | ||||
| 6. Round | 13/09/2008 | Leyton Orient | - | Stockport County | 0:3 | ||||
| 7. Round | 20/09/2008 | Leyton Orient | - | Leicester City | 1:3 | ||||
| 8. Round | 26/09/2008 | Southend United | - | Leyton Orient | 3:0 |  |
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| 9. Round | 04/10/2008 | Leyton Orient | - | Scunthorpe United | 2:2 | ||||
| 10. Round | 11/10/2008 | Bristol Rovers | - | Leyton Orient | 2:1 | ||||
| 11. Round | 18/10/2008 | Leyton Orient | - | Tranmere Rovers | 0:1 | ||||
| 15. Round | 01/11/2008 | Leyton Orient | - | Hartlepool United | 1:0 | |
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| 16. Round | 15/11/2008 | Crewe Alexandra | - | Leyton Orient | 0:2 | |
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| 23. Round | 28/12/2008 | Colchester United | - | Leyton Orient | 1:0 | ||||
| 30. Round | 07/04/2009 | Leyton Orient | - | Leeds United | 2:2 |
England