| 1. Round | 18/08/2012 | Gillingham FC | - | Bradford City | 3:1 | ||||
| 2. Round | 21/08/2012 | Wycombe Wanderers | - | Gillingham FC | 0:1 | ||||
| 8. Round | 22/09/2012 | Port Vale FC | - | Gillingham FC | 0:2 |  |
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| 9. Round | 29/09/2012 | Gillingham FC | - | Rochdale AFC | 1:2 |  |
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| 16. Round | 06/11/2012 | Gillingham FC | - | Cheltenham Town | 0:0 | ||||
| 17. Round | 10/11/2012 | Plymouth Argyle | - | Gillingham FC | 2:2 | ||||
| 18. Round | 17/11/2012 | Gillingham FC | - | Morecambe FC | 2:1 | ||||
| 19. Round | 20/11/2012 | Gillingham FC | - | Exeter City | 2:3 |  |
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| 20. Round | 24/11/2012 | Accrington Stanley | - | Gillingham FC | 1:1 | ||||
| 26. Round | 01/01/2013 | Southend United | - | Gillingham FC | 0:1 |
England