| 6. Round | 15/09/2012 | AFC Wimbledon | - | Rochdale AFC | 1:2 | ||||
| 7. Round | 18/09/2012 | AFC Wimbledon | - | Torquay United | 0:1 | ||||
| 8. Round | 22/09/2012 | Wycombe Wanderers | - | AFC Wimbledon | 0:1 | ||||
| 9. Round | 29/09/2012 | AFC Wimbledon | - | Accrington Stanley | 1:2 | ||||
| 10. Round | 02/10/2012 | Oxford United | - | AFC Wimbledon | 3:2 |  |
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| 11. Round | 06/10/2012 | Plymouth Argyle | - | AFC Wimbledon | 1:2 | ||||
| 12. Round | 13/10/2012 | AFC Wimbledon | - | Cheltenham Town | 1:2 | ||||
| 13. Round | 20/10/2012 | Fleetwood Town | - | AFC Wimbledon | 1:1 | |
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| 14. Round | 23/10/2012 | AFC Wimbledon | - | Bristol Rovers | 3:1 | ||||
| 15. Round | 27/10/2012 | AFC Wimbledon | - | Gillingham FC | 0:1 | ||||
| 16. Round | 06/11/2012 | Exeter City | - | AFC Wimbledon | 2:0 | ||||
| 17. Round | 10/11/2012 | York City | - | AFC Wimbledon | 0:3 | ||||
| 18. Round | 17/11/2012 | AFC Wimbledon | - | Aldershot Town | 1:1 | ||||
| 20. Round | 24/11/2012 | Morecambe FC | - | AFC Wimbledon | 3:1 | ||||
| 22. Round | 15/12/2012 | AFC Wimbledon | - | Rotherham United | 0:1 |
England