| 6. Round | 15/09/2012 | Gillingham FC | - | Bristol Rovers | 4:0 |  |
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| 7. Round | 18/09/2012 | Gillingham FC | - | Southend United | 1:0 | ||||
| 8. Round | 22/09/2012 | Port Vale FC | - | Gillingham FC | 0:2 | ||||
| 9. Round | 29/09/2012 | Gillingham FC | - | Rochdale AFC | 1:2 | ||||
| 10. Round | 02/10/2012 | Northampton Town | - | Gillingham FC | 1:2 | ||||
| 11. Round | 06/10/2012 | Oxford United | - | Gillingham FC | 0:0 | ||||
| 12. Round | 13/10/2012 | Gillingham FC | - | Aldershot Town | 4:0 |
England