| 1. Round | 09/08/2008 | Scunthorpe United | - | Leeds United | 1:2 | ||||
| 2. Round | 16/08/2008 | Walsall FC | - | Scunthorpe United | 2:1 | ||||
| 3. Round | 23/08/2008 | Scunthorpe United | - | Peterborough United | 1:0 | ||||
| 6. Round | 13/09/2008 | Scunthorpe United | - | Carlisle United | 2:1 | ||||
| 7. Round | 20/09/2008 | Hereford United | - | Scunthorpe United | 1:2 |  |
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| 8. Round | 27/09/2008 | Scunthorpe United | - | Yeovil Town | 2:0 |  |
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| 9. Round | 04/10/2008 | Leyton Orient | - | Scunthorpe United | 2:2 | |
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| 10. Round | 11/10/2008 | Scunthorpe United | - | Crewe Alexandra | 3:0 | |
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| 12. Round | 21/10/2008 | Scunthorpe United | - | Southend United | 1:1 | ||||
| 13. Round | 25/10/2008 | Scunthorpe United | - | Millwall FC | 3:2 | ||||
| 14. Round | 28/10/2008 | Oldham Athletic | - | Scunthorpe United | 3:0 | |
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| 15. Round | 01/11/2008 | Scunthorpe United | - | Swindon Town | 3:3 | ||||
| 16. Round | 14/11/2008 | Bristol Rovers | - | Scunthorpe United | 1:2 | |
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| 17. Round | 22/11/2008 | Scunthorpe United | - | Leicester City | 1:2 | ||||
| 18. Round | 25/11/2008 | Tranmere Rovers | - | Scunthorpe United | 2:0 | ||||
| 20. Round | 13/12/2008 | Scunthorpe United | - | Northampton Town | 4:4 |
England