| 1. Round | 05/08/2006 | Millwall FC | - | Yeovil Town | 1:1 | ||||
| 2. Round | 08/08/2006 | Leyton Orient | - | Millwall FC | 2:0 | ||||
| 3. Round | 12/08/2006 | Chesterfield FC | - | Millwall FC | 5:1 | ||||
| 4. Round | 19/08/2006 | Millwall FC | - | Oldham Athletic | 1:0 | ||||
| 5. Round | 26/08/2006 | Cheltenham Town | - | Millwall FC | 3:2 | ||||
| 6. Round | 02/09/2006 | Millwall FC | - | Blackpool FC | 0:0 |  |
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| 7. Round | 09/09/2006 | Millwall FC | - | Brighton & Hove Albion | 0:1 | ||||
| 8. Round | 12/09/2006 | Gillingham FC | - | Millwall FC | 2:1 | ||||
| 9. Round | 16/09/2006 | Crewe Alexandra | - | Millwall FC | 1:0 | |
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| 10. Round | 23/09/2006 | Millwall FC | - | Northampton Town | 0:1 | ||||
| 17. Round | 03/11/2006 | Tranmere Rovers | - | Millwall FC | 3:1 | |
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| 18. Round | 18/11/2006 | Millwall FC | - | Doncaster Rovers | 2:2 | |
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| 19. Round | 25/11/2006 | Nottingham Forest | - | Millwall FC | 3:1 | ||||
| 21. Round | 09/12/2006 | Millwall FC | - | Bradford City | 2:0 |
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