| 7. Round | 10/09/2016 | Scunthorpe United | - | Southend United | 4:0 |  |
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| 8. Round | 17/09/2016 | Shrewsbury Town | - | Scunthorpe United | 0:1 | ||||
| 6. Round | 20/09/2016 | Scunthorpe United | - | Charlton Athletic | 0:0 | ||||
| 9. Round | 24/09/2016 | Scunthorpe United | - | Sheffield United | 2:2 | ||||
| 10. Round | 27/09/2016 | Walsall FC | - | Scunthorpe United | 1:4 | ||||
| 11. Round | 01/10/2016 | Bury FC | - | Scunthorpe United | 1:2 | ||||
| 12. Round | 08/10/2016 | Scunthorpe United | - | Northampton Town | 1:1 | ||||
| 13. Round | 15/10/2016 | Scunthorpe United | - | Milton Keynes Dons | 2:1 | ||||
| 15. Round | 22/10/2016 | Chesterfield FC | - | Scunthorpe United | 0:3 | ||||
| 16. Round | 29/10/2016 | Scunthorpe United | - | Swindon Town | 4:1 | ||||
| 17. Round | 12/11/2016 | Coventry City | - | Scunthorpe United | 0:1 | ||||
| 18. Round | 19/11/2016 | Scunthorpe United | - | Oldham Athletic | 1:0 | ||||
| 19. Round | 22/11/2016 | Peterborough United | - | Scunthorpe United | 0:2 | ||||
| 20. Round | 26/11/2016 | Scunthorpe United | - | Oxford United | 1:1 | ||||
| 23. Round | 26/12/2016 | Bradford City | - | Scunthorpe United | 0:0 | ||||
| 26. Round | 07/01/2017 | Scunthorpe United | - | Bury FC | 3:2 |
England
