| 5. Round | 06/09/2008 | Carlisle United | - | Southend United | 2:1 |  |
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| 6. Round | 13/09/2008 | Southend United | - | Hereford United | 1:0 | ||||
| 7. Round | 20/09/2008 | Crewe Alexandra | - | Southend United | 3:4 | |
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| 8. Round | 26/09/2008 | Southend United | - | Leyton Orient | 3:0 | |
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| 20. Round | 13/12/2008 | Southend United | - | Huddersfield Town | 0:1 | ||||
| 22. Round | 26/12/2008 | Southend United | - | Northampton Town | 1:0 | ||||
| 23. Round | 28/12/2008 | Milton Keynes Dons | - | Southend United | 2:0 |  |
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| 26. Round | 17/01/2009 | Stockport County | - | Southend United | 3:1 | ||||
| 24. Round | 20/01/2009 | Leyton Orient | - | Southend United | 1:1 | ||||
| 29. Round | 31/01/2009 | Southend United | - | Bristol Rovers | 1:0 | |
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| 32. Round | 14/02/2009 | Southend United | - | Tranmere Rovers | 2:1 | ||||
| 25. Round | 17/02/2009 | Southend United | - | Crewe Alexandra | 0:1 | ||||
| 40. Round | 27/03/2009 | Southend United | - | Hartlepool United | 3:2 | ||||
| 42. Round | 10/04/2009 | Southend United | - | Milton Keynes Dons | 0:2 | ||||
| 44. Round | 18/04/2009 | Southend United | - | Leicester City | 0:2 | ||||
| 45. Round | 25/04/2009 | Oldham Athletic | - | Southend United | 1:1 |
Scotland
