| 27. Round | 05/01/2013 | Bristol Rovers | - | Gillingham FC | 0:2 | ||||
| 28. Round | 12/01/2013 | Gillingham FC | - | Port Vale FC | 1:2 | ||||
| 30. Round | 26/01/2013 | Gillingham FC | - | York City | 1:1 |  |
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| 25. Round | 29/01/2013 | Gillingham FC | - | Northampton Town | 2:0 | ||||
| 31. Round | 04/02/2013 | Gillingham FC | - | Wycombe Wanderers | 0:1 | ||||
| 34. Round | 23/02/2013 | Chesterfield FC | - | Gillingham FC | 0:1 | ||||
| 35. Round | 26/02/2013 | Gillingham FC | - | Oxford United | 0:1 | ||||
| 36. Round | 02/03/2013 | Aldershot Town | - | Gillingham FC | 1:1 | ||||
| 37. Round | 09/03/2013 | Gillingham FC | - | Plymouth Argyle | 2:1 | ||||
| 38. Round | 12/03/2013 | Exeter City | - | Gillingham FC | 0:0 | ||||
| 40. Round | 23/03/2013 | Gillingham FC | - | Accrington Stanley | 1:0 | ||||
| 42. Round | 01/04/2013 | Gillingham FC | - | Rotherham United | 1:0 | ||||
| 43. Round | 06/04/2013 | Gillingham FC | - | Torquay United | 1:0 | ||||
| 44. Round | 13/04/2013 | Cheltenham Town | - | Gillingham FC | 1:0 | ||||
| 45. Round | 20/04/2013 | Gillingham FC | - | AFC Wimbledon | 2:2 | ||||
| 46. Round | 27/04/2013 | Burton Albion | - | Gillingham FC | 3:2 |
England