| 6. Round | 03/09/1999 | Barnsley FC | - | Tranmere Rovers | 3:0 | ||||
| 7. Round | 11/09/1999 | Blackburn Rovers | - | Tranmere Rovers | 2:0 |  |
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| 8. Round | 18/09/1999 | Tranmere Rovers | - | Portsmouth FC | 2:4 | ||||
| 9. Round | 25/09/1999 | Tranmere Rovers | - | Charlton Athletic | 2:2 | ||||
| 10. Round | 03/10/1999 | Crewe Alexandra | - | Tranmere Rovers | 0:2 | ||||
| 11. Round | 09/10/1999 | Queens Park Rangers | - | Tranmere Rovers | 2:1 | ||||
| 12. Round | 16/10/1999 | Tranmere Rovers | - | Manchester City | 1:1 | ||||
| 14. Round | 23/10/1999 | Crystal Palace | - | Tranmere Rovers | 2:2 | ||||
| 17. Round | 06/11/1999 | Tranmere Rovers | - | West Bromwich Albion | 3:0 |
England