| 15. Round | 22/10/2016 | Peterborough United | - | AFC Wimbledon | 0:1 | ||||
| 17. Round | 12/11/2016 | Oldham Athletic | - | AFC Wimbledon | 0:0 | ||||
| 18. Round | 19/11/2016 | AFC Wimbledon | - | Bury FC | 5:1 | ||||
| 19. Round | 22/11/2016 | Millwall FC | - | AFC Wimbledon | 0:0 | ||||
| 20. Round | 26/11/2016 | AFC Wimbledon | - | Fleetwood Town | 2:2 | ||||
| 21. Round | 10/12/2016 | Milton Keynes Dons | - | AFC Wimbledon | 1:0 | ||||
| 22. Round | 17/12/2016 | AFC Wimbledon | - | Port Vale FC | 4:0 |  |
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| 23. Round | 26/12/2016 | Southend United | - | AFC Wimbledon | 3:0 | ||||
| 24. Round | 31/12/2016 | Bristol Rovers | - | AFC Wimbledon | 2:0 | ||||
| 28. Round | 21/01/2017 | Chesterfield FC | - | AFC Wimbledon | 0:0 | ||||
| 31. Round | 11/02/2017 | AFC Wimbledon | - | Charlton Athletic | 1:1 |  |
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| 32. Round | 14/02/2017 | AFC Wimbledon | - | Coventry City | 1:1 | ||||
| 37. Round | 11/03/2017 | AFC Wimbledon | - | Northampton Town | 0:1 |
Scotland