| 1. Round | 09/08/2008 | Swindon Town | - | Tranmere Rovers | 3:1 | ||||
| 2. Round | 16/08/2008 | Tranmere Rovers | - | Hartlepool United | 1:0 |  |
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| 3. Round | 23/08/2008 | Leicester City | - | Tranmere Rovers | 3:1 | ||||
| 4. Round | 30/08/2008 | Tranmere Rovers | - | Northampton Town | 4:1 | |
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| 5. Round | 06/09/2008 | Tranmere Rovers | - | Oldham Athletic | 0:1 |  |
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| 6. Round | 13/09/2008 | Huddersfield Town | - | Tranmere Rovers | 1:2 | ||||
| 7. Round | 20/09/2008 | Peterborough United | - | Tranmere Rovers | 2:2 | ||||
| 8. Round | 26/09/2008 | Tranmere Rovers | - | Colchester United | 3:4 | ||||
| 30. Round | 17/03/2009 | Cheltenham Town | - | Tranmere Rovers | 1:0 | ||||
| 40. Round | 28/03/2009 | Brighton & Hove Albion | - | Tranmere Rovers | 0:0 | ||||
| 41. Round | 05/04/2009 | Tranmere Rovers | - | Bristol Rovers | 2:0 | ||||
| 42. Round | 11/04/2009 | Walsall FC | - | Tranmere Rovers | 0:1 | ||||
| 44. Round | 18/04/2009 | Leeds United | - | Tranmere Rovers | 3:1 | ||||
| 45. Round | 25/04/2009 | Tranmere Rovers | - | Yeovil Town | 1:1 | ||||
| 46. Round | 02/05/2009 | Scunthorpe United | - | Tranmere Rovers | 1:1 | |
England