| 8. Round | 19/09/2009 | Brighton & Hove Albion | - | Southend United | 2:3 | ||||
| 9. Round | 26/09/2009 | Southend United | - | Oldham Athletic | 0:1 | ||||
| 10. Round | 29/09/2009 | Brentford FC | - | Southend United | 2:1 | ||||
| 11. Round | 03/10/2009 | Stockport County | - | Southend United | 0:2 | ||||
| 12. Round | 09/10/2009 | Southend United | - | Southampton FC | 1:3 | ||||
| 27. Round | 16/01/2010 | Huddersfield Town | - | Southend United | 2:1 | ||||
| 28. Round | 23/01/2010 | Southend United | - | Wycombe Wanderers | 1:1 | ||||
| 25. Round | 26/01/2010 | Millwall FC | - | Southend United | 2:0 | ||||
| 37. Round | 20/03/2010 | Southend United | - | Carlisle United | 2:2 | ||||
| 26. Round | 23/03/2010 | Southend United | - | Walsall FC | 3:0 | ||||
| 40. Round | 05/04/2010 | Gillingham FC | - | Southend United | 3:0 | ||||
| 41. Round | 10/04/2010 | Leeds United | - | Southend United | 2:0 |
England