| 1. Round | 05/08/2006 | Port Vale FC | - | Leyton Orient | 3:0 | ||||
| 2. Round | 08/08/2006 | Leyton Orient | - | Millwall FC | 2:0 | ||||
| 3. Round | 12/08/2006 | Leyton Orient | - | AFC Bournemouth | 3:2 | ||||
| 4. Round | 19/08/2006 | Carlisle United | - | Leyton Orient | 3:1 | ||||
| 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 |  |
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| 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 | ||||
| 13. Round | 07/10/2006 | Leyton Orient | - | Chesterfield FC | 0:0 | ||||
| 14. Round | 14/10/2006 | Oldham Athletic | - | Leyton Orient | 3:3 | ||||
| 15. Round | 21/10/2006 | Leyton Orient | - | Cheltenham Town | 2:0 | ||||
| 16. Round | 28/10/2006 | Scunthorpe United | - | Leyton Orient | 3:1 |
England