| 13. Round | 15/10/2016 | Scunthorpe United | - | Milton Keynes Dons | 2:1 | ||||
| 14. Round | 18/10/2016 | Oldham Athletic | - | Scunthorpe United | 2:0 | ||||
| 41. Round | 01/04/2017 | Millwall FC | - | Scunthorpe United | 3:1 | ||||
| 42. Round | 08/04/2017 | Scunthorpe United | - | Bolton Wanderers | 1:0 | ||||
| 43. Round | 14/04/2017 | Milton Keynes Dons | - | Scunthorpe United | 0:1 | ||||
| 44. Round | 17/04/2017 | Scunthorpe United | - | Chesterfield FC | 3:1 | ||||
| 45. Round | 22/04/2017 | Swindon Town | - | Scunthorpe United | 1:2 | ||||
| 46. Round | 30/04/2017 | Scunthorpe United | - | Coventry City | 3:1 |
England