| 2. Round | 21/08/2012 | Wycombe Wanderers | - | Gillingham FC | 0:1 | ||||
| 3. Round | 25/08/2012 | Dagenham & Redbridge | - | Gillingham FC | 1:2 | ||||
| 5. Round | 08/09/2012 | Barnet FC | - | Gillingham FC | 1:3 |  |
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| 6. Round | 15/09/2012 | Gillingham FC | - | Bristol Rovers | 4:0 | ||||
| 7. Round | 18/09/2012 | Gillingham FC | - | Southend United | 1:0 | ||||
| 14. Round | 23/10/2012 | Torquay United | - | Gillingham FC | 2:1 | ||||
| 16. Round | 06/11/2012 | Gillingham FC | - | Cheltenham Town | 0:0 | ||||
| 18. Round | 17/11/2012 | Gillingham FC | - | Morecambe FC | 2:1 | ||||
| 19. Round | 20/11/2012 | Gillingham FC | - | Exeter City | 2:3 | ||||
| 20. Round | 24/11/2012 | Accrington Stanley | - | Gillingham FC | 1:1 | ||||
| 24. Round | 26/12/2012 | Gillingham FC | - | Barnet FC | 0:1 | ||||
| 34. Round | 23/02/2013 | Chesterfield FC | - | Gillingham FC | 0:1 | ||||
| 41. Round | 30/03/2013 | Fleetwood Town | - | Gillingham FC | 2:2 | ||||
| 46. Round | 27/04/2013 | Burton Albion | - | Gillingham FC | 3:2 |
England