| 26. Round | 02/01/2006 | Tranmere Rovers | - | Rotherham United | 3:2 | ||||
| 27. Round | 07/01/2006 | Tranmere Rovers | - | AFC Bournemouth | 0:0 | ||||
| 28. Round | 14/01/2006 | Hartlepool United | - | Tranmere Rovers | 0:0 | ||||
| 29. Round | 21/01/2006 | Tranmere Rovers | - | Southend United | 0:0 | ||||
| 30. Round | 28/01/2006 | Bradford City | - | Tranmere Rovers | 0:0 |  |
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| 31. Round | 03/02/2006 | Tranmere Rovers | - | Huddersfield Town | 2:1 | ||||
| 32. Round | 11/02/2006 | Gillingham FC | - | Tranmere Rovers | 1:1 | |
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| 33. Round | 14/02/2006 | Tranmere Rovers | - | Hartlepool United | 0:0 | ||||
| 34. Round | 18/02/2006 | Tranmere Rovers | - | Barnsley FC | 0:1 | ||||
| 35. Round | 25/02/2006 | Oldham Athletic | - | Tranmere Rovers | 1:0 | ||||
| 36. Round | 07/03/2006 | Swindon Town | - | Tranmere Rovers | 1:2 | ||||
| 37. Round | 11/03/2006 | Tranmere Rovers | - | Chesterfield FC | 4:1 | ||||
| 38. Round | 17/03/2006 | Tranmere Rovers | - | Walsall FC | 1:2 |
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