| 16. Round | 06/11/2012 | Walsall FC | - | Scunthorpe United | 1:4 | ||||
| 17. Round | 10/11/2012 | Coventry City | - | Scunthorpe United | 1:2 | ||||
| 18. Round | 17/11/2012 | Scunthorpe United | - | Notts County | 2:2 |  |
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| 19. Round | 20/11/2012 | Scunthorpe United | - | Bury FC | 1:2 | ||||
| 20. Round | 24/11/2012 | Doncaster Rovers | - | Scunthorpe United | 4:0 | ||||
| 21. Round | 08/12/2012 | Scunthorpe United | - | AFC Bournemouth | 1:2 | ||||
| 22. Round | 15/12/2012 | Leyton Orient | - | Scunthorpe United | 1:3 | |
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| 24. Round | 26/12/2012 | Sheffield United | - | Scunthorpe United | 3:0 | ||||
| 25. Round | 29/12/2012 | Tranmere Rovers | - | Scunthorpe United | 1:0 | ||||
| 26. Round | 01/01/2013 | Scunthorpe United | - | Oldham Athletic | 2:2 |  |
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| 27. Round | 05/01/2013 | Scunthorpe United | - | Shrewsbury Town | 0:0 |
France