| 1. Round | 09/08/2008 | Oldham Athletic | - | Millwall FC | 4:3 |  |
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| 2. Round | 16/08/2008 | Millwall FC | - | Southend United | 1:1 | ||||
| 4. Round | 30/08/2008 | Millwall FC | - | Huddersfield Town | 2:1 | |
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| 6. Round | 13/09/2008 | Leicester City | - | Millwall FC | 0:1 |  |
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| 10. Round | 11/10/2008 | Tranmere Rovers | - | Millwall FC | 1:3 | |
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| 12. Round | 21/10/2008 | Colchester United | - | Millwall FC | 1:2 | ||||
| 13. Round | 25/10/2008 | Scunthorpe United | - | Millwall FC | 3:2 | ||||
| 14. Round | 28/10/2008 | Millwall FC | - | Hereford United | 1:0 | ||||
| 15. Round | 01/11/2008 | Brighton & Hove Albion | - | Millwall FC | 4:1 | |
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| 16. Round | 15/11/2008 | Millwall FC | - | Stockport County | 1:0 | ||||
| 17. Round | 22/11/2008 | Leyton Orient | - | Millwall FC | 0:0 | ||||
| 18. Round | 25/11/2008 | Millwall FC | - | Carlisle United | 1:0 | |
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| 19. Round | 06/12/2008 | Millwall FC | - | Bristol Rovers | 3:2 | |
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| 20. Round | 13/12/2008 | Walsall FC | - | Millwall FC | 1:2 | ||||
| 21. Round | 20/12/2008 | Millwall FC | - | Crewe Alexandra | 0:0 | ||||
| 22. Round | 26/12/2008 | Peterborough United | - | Millwall FC | 1:0 | ||||
| 23. Round | 28/12/2008 | Millwall FC | - | Yeovil Town | 1:1 | ||||
| 26. Round | 17/01/2009 | Millwall FC | - | Tranmere Rovers | 1:0 |
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