| 1. Round | 07/08/1999 | Tranmere Rovers | - | Bolton Wanderers | 0:0 | ||||
| 3. Round | 21/08/1999 | Tranmere Rovers | - | Huddersfield Town | 1:0 |  |
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| 4. Round | 28/08/1999 | Port Vale FC | - | Tranmere Rovers | 1:0 | ||||
| 5. Round | 30/08/1999 | Tranmere Rovers | - | Sheffield United | 1:3 | ||||
| 6. Round | 03/09/1999 | Barnsley FC | - | Tranmere Rovers | 3:0 | ||||
| 8. Round | 18/09/1999 | Tranmere Rovers | - | Portsmouth FC | 2:4 | ||||
| 10. Round | 03/10/1999 | Crewe Alexandra | - | Tranmere Rovers | 0:2 | ||||
| 13. Round | 19/10/1999 | Tranmere Rovers | - | Grimsby Town | 3:2 | ||||
| 15. Round | 26/10/1999 | Charlton Athletic | - | Tranmere Rovers | 3:2 | ||||
| 17. Round | 06/11/1999 | Tranmere Rovers | - | West Bromwich Albion | 3:0 | ||||
| 18. Round | 12/11/1999 | Ipswich Town | - | Tranmere Rovers | 0:0 | ||||
| 28. Round | 22/01/2000 | Huddersfield Town | - | Tranmere Rovers | 1:0 | ||||
| 30. Round | 05/02/2000 | Sheffield United | - | Tranmere Rovers | 3:1 | ||||
| 31. Round | 11/02/2000 | Tranmere Rovers | - | Barnsley FC | 2:2 | ||||
| 32. Round | 16/02/2000 | Wolverhampton Wanderers | - | Tranmere Rovers | 4:0 |
England