| 3. Round | 12/08/2006 | Leyton Orient | - | AFC Bournemouth | 3:2 | ||||
| 5. Round | 26/08/2006 | Leyton Orient | - | Swansea City | 0:1 | ||||
| 6. Round | 02/09/2006 | Tranmere Rovers | - | Leyton Orient | 3:0 | ||||
| 7. Round | 09/09/2006 | Leyton Orient | - | Brentford FC | 1:1 | ||||
| 8. Round | 12/09/2006 | Bristol City | - | Leyton Orient | 2:1 | ||||
| 10. Round | 23/09/2006 | Leyton Orient | - | Rotherham United | 2:3 | ||||
| 11. Round | 26/09/2006 | Leyton Orient | - | Gillingham FC | 3:3 | ||||
| 12. Round | 30/09/2006 | Blackpool FC | - | Leyton Orient | 3:0 | ||||
| 15. Round | 21/10/2006 | Leyton Orient | - | Cheltenham Town | 2:0 | ||||
| 16. Round | 28/10/2006 | Scunthorpe United | - | Leyton Orient | 3:1 | ||||
| 17. Round | 04/11/2006 | Doncaster Rovers | - | Leyton Orient | 0:0 | ||||
| 18. Round | 18/11/2006 | Leyton Orient | - | Yeovil Town | 0:0 | ||||
| 20. Round | 05/12/2006 | Leyton Orient | - | Bradford City | 1:2 | ||||
| 19. Round | 19/12/2006 | Northampton Town | - | Leyton Orient | 0:1 |  |
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| 23. Round | 23/12/2006 | Leyton Orient | - | Crewe Alexandra | 1:1 | ||||
| 24. Round | 26/12/2006 | Gillingham FC | - | Leyton Orient | 2:1 | ||||
| 26. Round | 01/01/2007 | Leyton Orient | - | Bristol City | 1:1 | ||||
| 28. Round | 13/01/2007 | Brentford FC | - | Leyton Orient | 2:2 | |
England