| 2. Round | 21/08/2012 | Burton Albion | - | AFC Wimbledon | 6:2 | ||||
| 3. Round | 25/08/2012 | Bradford City | - | AFC Wimbledon | 5:1 |  |
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| 4. Round | 01/09/2012 | AFC Wimbledon | - | Dagenham & Redbridge | 2:2 | ||||
| 8. Round | 22/09/2012 | Wycombe Wanderers | - | AFC Wimbledon | 0:1 | |
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| 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 | ||||
| 19. Round | 20/11/2012 | AFC Wimbledon | - | Southend United | 0:4 | ||||
| 20. Round | 24/11/2012 | Morecambe FC | - | AFC Wimbledon | 3:1 | |
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| 21. Round | 08/12/2012 | Barnet FC | - | AFC Wimbledon | 1:1 | ||||
| 22. Round | 15/12/2012 | AFC Wimbledon | - | Rotherham United | 0:1 | |
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| 30. Round | 24/01/2013 | AFC Wimbledon | - | Port Vale FC | 2:2 | ||||
| 23. Round | 05/02/2013 | Port Vale FC | - | AFC Wimbledon | 3:0 | ||||
| 32. Round | 09/02/2013 | Chesterfield FC | - | AFC Wimbledon | 2:0 | |
England