| 4. Round | 01/09/2012 | Hartlepool United | - | Scunthorpe United | 2:0 | ||||
| 5. Round | 08/09/2012 | Scunthorpe United | - | Sheffield United | 1:1 |  |
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| 6. Round | 15/09/2012 | Shrewsbury Town | - | Scunthorpe United | 0:1 | |
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| 7. Round | 18/09/2012 | Oldham Athletic | - | Scunthorpe United | 1:1 | ||||
| 8. Round | 22/09/2012 | Scunthorpe United | - | Colchester United | 1:0 | ||||
| 9. Round | 29/09/2012 | Portsmouth FC | - | Scunthorpe United | 2:1 | |
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| 10. Round | 02/10/2012 | Scunthorpe United | - | Tranmere Rovers | 1:3 | |
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| 12. Round | 13/10/2012 | Scunthorpe United | - | Brentford FC | 1:1 | ||||
| 13. Round | 20/10/2012 | Swindon Town | - | Scunthorpe United | 1:1 | |
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| 14. Round | 23/10/2012 | Scunthorpe United | - | Preston North End | 2:3 | ||||
| 15. Round | 27/10/2012 | Scunthorpe United | - | Milton Keynes Dons | 0:3 | ||||
| 16. Round | 06/11/2012 | Walsall FC | - | Scunthorpe United | 1:4 |  |
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| 20. Round | 24/11/2012 | Doncaster Rovers | - | Scunthorpe United | 4:0 |
England
