| 2. Round | 13/08/2011 | Accrington Stanley | - | Southend United | 1:2 | ||||
| 5. Round | 27/08/2011 | Port Vale FC | - | Southend United | 2:3 |  |
|||
| 6. Round | 03/09/2011 | Southend United | - | Northampton Town | 2:2 | ||||
| 7. Round | 10/09/2011 | Swindon Town | - | Southend United | 2:0 | ||||
| 9. Round | 17/09/2011 | Southend United | - | Plymouth Argyle | 2:0 |  |
|||
| 10. Round | 24/09/2011 | Rotherham United | - | Southend United | 0:4 | ||||
| 11. Round | 30/09/2011 | Southend United | - | Shrewsbury Town | 3:0 | ||||
| 12. Round | 08/10/2011 | Crewe Alexandra | - | Southend United | 1:3 | ||||
| 13. Round | 15/10/2011 | Southend United | - | Morecambe FC | 1:1 | ||||
| 14. Round | 22/10/2011 | Southend United | - | Torquay United | 4:1 | ||||
| 15. Round | 25/10/2011 | Barnet FC | - | Southend United | 0:3 | ||||
| 16. Round | 29/10/2011 | Macclesfield Town | - | Southend United | 0:2 | ||||
| 17. Round | 05/11/2011 | Southend United | - | Oxford United | 2:1 | ||||
| 20. Round | 10/12/2011 | Cheltenham Town | - | Southend United | 3:0 | ||||
| 21. Round | 16/12/2011 | Southend United | - | Bradford City | 0:1 | ||||
| 23. Round | 31/12/2011 | AFC Wimbledon | - | Southend United | 1:4 | ||||
| 24. Round | 02/01/2012 | Southend United | - | Dagenham & Redbridge | 1:1 |
England