| 15. Round | 01/11/2008 | Milton Keynes Dons | - | Tranmere Rovers | 1:0 | ||||
| 16. Round | 15/11/2008 | Tranmere Rovers | - | Southend United | 2:2 | ||||
| 17. Round | 22/11/2008 | Yeovil Town | - | Tranmere Rovers | 1:0 | ||||
| 23. Round | 28/12/2008 | Tranmere Rovers | - | Walsall FC | 2:1 | ||||
| 32. Round | 14/02/2009 | Southend United | - | Tranmere Rovers | 2:1 | ||||
| 25. Round | 17/02/2009 | Tranmere Rovers | - | Peterborough United | 1:1 | ||||
| 33. Round | 21/02/2009 | Tranmere Rovers | - | Milton Keynes Dons | 1:1 | ||||
| 38. Round | 14/03/2009 | Tranmere Rovers | - | Huddersfield Town | 3:1 | ||||
| 39. Round | 21/03/2009 | Oldham Athletic | - | Tranmere Rovers | 0:2 | ||||
| 40. Round | 28/03/2009 | Brighton & Hove Albion | - | Tranmere Rovers | 0:0 | ||||
| 41. Round | 05/04/2009 | Tranmere Rovers | - | Bristol Rovers | 2:0 |  |
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| 42. Round | 11/04/2009 | Walsall FC | - | Tranmere Rovers | 0:1 | ||||
| 46. Round | 02/05/2009 | Scunthorpe United | - | Tranmere Rovers | 1:1 |
England