| 8. Round | 26/09/2008 | Southend United | - | Leyton Orient | 3:0 | ||||
| 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 | ||||
| 21. Round | 20/12/2008 | Oldham Athletic | - | Leyton Orient | 1:1 | ||||
| 23. Round | 28/12/2008 | Colchester United | - | Leyton Orient | 1:0 |  |
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| 25. Round | 10/01/2009 | Leicester City | - | Leyton Orient | 3:0 | ||||
| 24. Round | 20/01/2009 | Leyton Orient | - | Southend United | 1:1 | ||||
| 27. Round | 24/01/2009 | Scunthorpe United | - | Leyton Orient | 2:1 | ||||
| 28. Round | 27/01/2009 | Milton Keynes Dons | - | Leyton Orient | 1:2 | ||||
| 34. Round | 28/02/2009 | Hereford United | - | Leyton Orient | 2:1 | ||||
| 35. Round | 03/03/2009 | Leyton Orient | - | Peterborough United | 2:3 | ||||
| 30. Round | 07/04/2009 | Leyton Orient | - | Leeds United | 2:2 |
England