| 15. Round | 22/10/2016 | Peterborough United | - | AFC Wimbledon | 0:1 | ||||
| 16. Round | 29/10/2016 | AFC Wimbledon | - | Bradford City | 2:3 | ||||
| 18. Round | 19/11/2016 | AFC Wimbledon | - | Bury FC | 5:1 | ||||
| 26. Round | 21/02/2017 | Gillingham FC | - | AFC Wimbledon | 2:2 | ||||
| 35. Round | 28/02/2017 | Scunthorpe United | - | AFC Wimbledon | 1:2 | ||||
| 36. Round | 04/03/2017 | Bolton Wanderers | - | AFC Wimbledon | 1:1 | ||||
| 37. Round | 11/03/2017 | AFC Wimbledon | - | Northampton Town | 0:1 | ||||
| 39. Round | 18/03/2017 | Fleetwood Town | - | AFC Wimbledon | 0:0 |  |
|||
| 40. Round | 25/03/2017 | AFC Wimbledon | - | Southend United | 0:2 | ||||
| 42. Round | 08/04/2017 | AFC Wimbledon | - | Bristol Rovers | 0:1 | ||||
| 45. Round | 22/04/2017 | Bradford City | - | AFC Wimbledon | 3:0 | ||||
| 46. Round | 30/04/2017 | AFC Wimbledon | - | Oldham Athletic | 0:0 |
England