| 30. Round | 31/01/2009 | Burnley FC | - | Charlton Athletic | 2:1 |  |
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| 31. Round | 03/02/2009 | Bristol City | - | Charlton Athletic | 2:1 | ||||
| 33. Round | 14/02/2009 | Charlton Athletic | - | Plymouth Argyle | 2:0 | ||||
| 34. Round | 21/02/2009 | Barnsley FC | - | Charlton Athletic | 0:0 | ||||
| 37. Round | 07/03/2009 | Charlton Athletic | - | Watford FC | 2:3 |  |
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| 38. Round | 10/03/2009 | Reading FC | - | Charlton Athletic | 2:2 | |
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| 39. Round | 14/03/2009 | Wolverhampton Wanderers | - | Charlton Athletic | 2:1 | ||||
| 40. Round | 21/03/2009 | Charlton Athletic | - | Preston North End | 0:0 | ||||
| 41. Round | 04/04/2009 | Southampton FC | - | Charlton Athletic | 2:3 | |
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| 42. Round | 11/04/2009 | Charlton Athletic | - | Birmingham City | 0:0 | ||||
| 43. Round | 13/04/2009 | Coventry City | - | Charlton Athletic | 0:0 | ||||
| 32. Round | 21/04/2009 | Charlton Athletic | - | Cardiff City | 2:2 | ||||
| 45. Round | 25/04/2009 | Derby County | - | Charlton Athletic | 1:0 |
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