| 29. Round | 30/01/2010 | Southend United | - | Swindon Town | 2:2 | ||||
| 31. Round | 13/02/2010 | Southend United | - | Tranmere Rovers | 1:1 |  |
|||
| 32. Round | 20/02/2010 | Milton Keynes Dons | - | Southend United | 3:1 | ||||
| 33. Round | 23/02/2010 | Norwich City | - | Southend United | 2:1 | |
|||
| 34. Round | 26/02/2010 | Southend United | - | Charlton Athletic | 1:2 | ||||
| 35. Round | 06/03/2010 | Hartlepool United | - | Southend United | 3:0 | ||||
| 36. Round | 13/03/2010 | Southend United | - | Exeter City | 0:0 | ||||
| 37. Round | 20/03/2010 | Southend United | - | Carlisle United | 2:2 | ||||
| 26. Round | 23/03/2010 | Southend United | - | Walsall FC | 3:0 | ||||
| 38. Round | 27/03/2010 | Bristol Rovers | - | Southend United | 4:3 | |
|||
| 39. Round | 03/04/2010 | Southend United | - | Yeovil Town | 0:0 | ||||
| 40. Round | 05/04/2010 | Gillingham FC | - | Southend United | 3:0 | ||||
| 41. Round | 10/04/2010 | Leeds United | - | Southend United | 2:0 | ||||
| 42. Round | 13/04/2010 | Southend United | - | Brentford FC | 2:2 | ||||
| 43. Round | 17/04/2010 | Southend United | - | Brighton & Hove Albion | 0:1 | ||||
| 44. Round | 24/04/2010 | Oldham Athletic | - | Southend United | 2:2 | ||||
| 45. Round | 01/05/2010 | Southend United | - | Stockport County | 2:1 |
England