| 31. Round | 04/02/2006 | Yeovil Town | - | Southend United | 0:2 | ||||
| 32. Round | 10/02/2006 | Southend United | - | Rotherham United | 2:0 | ||||
| 33. Round | 14/02/2006 | Brentford FC | - | Southend United | 2:0 | ||||
| 34. Round | 18/02/2006 | Chesterfield FC | - | Southend United | 3:4 | ||||
| 35. Round | 25/02/2006 | Southend United | - | Walsall FC | 0:0 | ||||
| 36. Round | 04/03/2006 | Colchester United | - | Southend United | 0:3 | ||||
| 37. Round | 10/03/2006 | Southend United | - | Scunthorpe United | 3:0 |  |
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| 38. Round | 18/03/2006 | Milton Keynes Dons | - | Southend United | 2:1 | ||||
| 39. Round | 25/03/2006 | Southend United | - | Hartlepool United | 3:0 |  |
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| 41. Round | 08/04/2006 | Southend United | - | Blackpool FC | 2:1 | ||||
| 42. Round | 14/04/2006 | Southend United | - | Gillingham FC | 0:1 | ||||
| 43. Round | 17/04/2006 | Barnsley FC | - | Southend United | 2:2 | ||||
| 44. Round | 22/04/2006 | Southend United | - | Doncaster Rovers | 0:1 | ||||
| 45. Round | 29/04/2006 | Swansea City | - | Southend United | 2:2 | ||||
| 46. Round | 06/05/2006 | Southend United | - | Bristol City | 1:0 |
England