| 1. Round | 03/08/1998 | Viktoria Plzeň | - | AC Sparta Praha | 0:1 | ||||
| 3. Round | 22/08/1998 | Viktoria Plzeň | - | Sigma Olomouc | 1:0 | ||||
| 5. Round | 13/09/1998 | FC Petra Drnovice | - | Viktoria Plzeň | 1:0 | ||||
| 10. Round | 25/10/1998 | Viktoria Plzeň | - | Chmel Blsany | 2:1 | ||||
| 12. Round | 07/11/1998 | Viktoria Plzeň | - | Baník Ostrava | 1:1 | ||||
| 15. Round | 28/11/1998 | FK Jablonec 97 | - | Viktoria Plzeň | 2:0 |  |
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| 25. Round | 02/05/1999 | Chmel Blsany | - | Viktoria Plzeň | 1:1 | ||||
| 26. Round | 09/05/1999 | Viktoria Plzeň | - | FC Dukla Pribram | 2:1 | ||||
| 27. Round | 12/05/1999 | Baník Ostrava | - | Viktoria Plzeň | 0:1 | ||||
| 29. Round | 22/05/1999 | Viktoria Žižkov | - | Viktoria Plzeň | 3:0 | ||||
| 30. Round | 30/05/1999 | Viktoria Plzeň | - | FK Jablonec 97 | 2:3 |
Czech Republic