| 1. Round | 06/08/2016 | Walsall FC | - | AFC Wimbledon | 3:1 | ||||
| 3. Round | 16/08/2016 | AFC Wimbledon | - | Scunthorpe United | 1:2 | ||||
| 4. Round | 20/08/2016 | Northampton Town | - | AFC Wimbledon | 0:0 | ||||
| 5. Round | 27/08/2016 | Rochdale AFC | - | AFC Wimbledon | 1:1 | ||||
| 7. Round | 10/09/2016 | AFC Wimbledon | - | Sheffield United | 2:3 | ||||
| 8. Round | 17/09/2016 | Charlton Athletic | - | AFC Wimbledon | 1:2 | ||||
| 9. Round | 24/09/2016 | AFC Wimbledon | - | Shrewsbury Town | 1:1 | ||||
| 13. Round | 15/10/2016 | AFC Wimbledon | - | Swindon Town | 0:0 | ||||
| 15. Round | 22/10/2016 | Peterborough United | - | AFC Wimbledon | 0:1 | ||||
| 16. Round | 29/10/2016 | AFC Wimbledon | - | Bradford City | 2:3 | ||||
| 17. Round | 12/11/2016 | Oldham Athletic | - | AFC Wimbledon | 0:0 | ||||
| 18. Round | 19/11/2016 | AFC Wimbledon | - | Bury FC | 5:1 |  |
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| 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 |  |
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| 27. Round | 14/01/2017 | AFC Wimbledon | - | Oxford United | 2:1 | ||||
| 28. Round | 21/01/2017 | Chesterfield FC | - | AFC Wimbledon | 0:0 |
England