| 14. Round | 23/10/2012 | Southend United | - | Aldershot Town | 1:2 | ||||
| 15. Round | 27/10/2012 | Southend United | - | York City | 0:0 | ||||
| 28. Round | 12/01/2013 | Exeter City | - | Southend United | 3:0 |  |
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| 32. Round | 09/02/2013 | Accrington Stanley | - | Southend United | 1:1 | ||||
| 27. Round | 12/02/2013 | Southend United | - | Cheltenham Town | 1:2 |
England