| 7. Round | 20/09/2008 | Aldershot Town | - | Gillingham FC | 2:1 | ||||
| 8. Round | 27/09/2008 | Gillingham FC | - | Port Vale FC | 1:0 | ||||
| 12. Round | 21/10/2008 | Gillingham FC | - | Notts County | 2:2 | ||||
| 16. Round | 15/11/2008 | Gillingham FC | - | Rotherham United | 4:0 |  |
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| 17. Round | 22/11/2008 | Bury FC | - | Gillingham FC | 4:0 | ||||
| 26. Round | 17/01/2009 | Morecambe FC | - | Gillingham FC | 0:1 | ||||
| 27. Round | 24/01/2009 | Gillingham FC | - | Exeter City | 1:0 |
England