| 15. Round | 22/10/2016 | Chesterfield FC | - | Scunthorpe United | 0:3 | ||||
| 16. Round | 29/10/2016 | Scunthorpe United | - | Swindon Town | 4:1 | ||||
| 31. Round | 11/02/2017 | Scunthorpe United | - | Shrewsbury Town | 0:1 | ||||
| 32. Round | 14/02/2017 | Scunthorpe United | - | Walsall FC | 0:0 | ||||
| 33. Round | 18/02/2017 | Sheffield United | - | Scunthorpe United | 1:1 | ||||
| 34. Round | 25/02/2017 | Bristol Rovers | - | Scunthorpe United | 1:1 |  |
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| 41. Round | 01/04/2017 | Millwall FC | - | Scunthorpe United | 3:1 | |
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| 46. Round | 30/04/2017 | Scunthorpe United | - | Coventry City | 3:1 |
England