| 28. Round | 23/01/2010 | Southend United | - | Wycombe Wanderers | 1:1 | ||||
| 25. Round | 26/01/2010 | Millwall FC | - | Southend United | 2:0 | ||||
| 30. Round | 08/02/2010 | Colchester United | - | Southend United | 2:0 | ||||
| 32. Round | 20/02/2010 | Milton Keynes Dons | - | Southend United | 3:1 |  |
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| 33. Round | 23/02/2010 | Norwich City | - | Southend United | 2:1 | ||||
| 34. Round | 26/02/2010 | Southend United | - | Charlton Athletic | 1:2 | |
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| 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 | ||||
| 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 | ||||
| 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 | ||||
| 46. Round | 08/05/2010 | Southampton FC | - | Southend United | 3:1 |
Scotland