| 32. Round | 14/02/2017 | Bury FC | - | Milton Keynes Dons | 0:0 | ||||
| 33. Round | 18/02/2017 | Milton Keynes Dons | - | Fleetwood Town | 0:1 | ||||
| 37. Round | 11/03/2017 | Milton Keynes Dons | - | Rochdale AFC | 2:2 | ||||
| 38. Round | 14/03/2017 | AFC Wimbledon | - | Milton Keynes Dons | 2:0 | ||||
| 44. Round | 17/04/2017 | Southend United | - | Milton Keynes Dons | 1:2 | ||||
| 46. Round | 30/04/2017 | Walsall FC | - | Milton Keynes Dons | 1:4 |
England