| 27. Round | 14/01/2017 | Northampton Town | - | Scunthorpe United | 1:2 | ||||
| 29. Round | 28/01/2017 | Scunthorpe United | - | Port Vale FC | 3:2 | ||||
| 30. Round | 04/02/2017 | Southend United | - | Scunthorpe United | 3:1 | ||||
| 33. Round | 18/02/2017 | Sheffield United | - | Scunthorpe United | 1:1 | ||||
| 35. Round | 28/02/2017 | Scunthorpe United | - | AFC Wimbledon | 1:2 | ||||
| 36. Round | 04/03/2017 | Scunthorpe United | - | Fleetwood Town | 0:2 | ||||
| 28. Round | 07/03/2017 | Charlton Athletic | - | Scunthorpe United | 2:1 | ||||
| 37. Round | 11/03/2017 | Gillingham FC | - | Scunthorpe United | 3:2 | ||||
| 38. Round | 14/03/2017 | Scunthorpe United | - | Rochdale AFC | 2:1 |  |
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| 40. Round | 26/03/2017 | Scunthorpe United | - | Bradford City | 3:2 | |
 |
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| 41. Round | 01/04/2017 | Millwall FC | - | Scunthorpe United | 3:1 | |
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| 42. Round | 08/04/2017 | Scunthorpe United | - | Bolton Wanderers | 1:0 |
England