| 15. Round | 31/10/2009 | Millwall FC | - | Colchester United | 2:1 | ||||
| 17. Round | 21/11/2009 | Oldham Athletic | - | Colchester United | 2:2 | ||||
| 18. Round | 24/11/2009 | Colchester United | - | Stockport County | 2:0 | ||||
| 19. Round | 01/12/2009 | Brentford FC | - | Colchester United | 1:0 | ||||
| 20. Round | 05/12/2009 | Colchester United | - | Bristol Rovers | 1:0 | ||||
| 21. Round | 11/12/2009 | Brighton & Hove Albion | - | Colchester United | 1:2 | ||||
| 23. Round | 26/12/2009 | Southend United | - | Colchester United | 1:2 |  |
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| 24. Round | 28/12/2009 | Colchester United | - | Southampton FC | 2:1 | ||||
| 28. Round | 23/01/2010 | Gillingham FC | - | Colchester United | 0:0 | ||||
| 44. Round | 24/04/2010 | Colchester United | - | Tranmere Rovers | 1:1 | ||||
| 45. Round | 01/05/2010 | Huddersfield Town | - | Colchester United | 2:1 | |
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| 46. Round | 08/05/2010 | Colchester United | - | Leyton Orient | 1:0 |
England