| 1. Round | 01/08/1999 | Dynamo České Budějovice | - | FC Petra Drnovice | 2:0 |  |
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| 2. Round | 08/08/1999 | Viktoria Žižkov | - | Dynamo České Budějovice | 1:1 | ||||
| 3. Round | 14/08/1999 | Dynamo České Budějovice | - | SFC Opava | 1:0 | |
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| 4. Round | 22/08/1999 | FK Jablonec 97 | - | Dynamo České Budějovice | 2:1 |  |
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| 5. Round | 29/08/1999 | Dynamo České Budějovice | - | FK Teplice | 3:1 | ||||
| 6. Round | 11/09/1999 | AC Sparta Praha | - | Dynamo České Budějovice | 7:0 | ||||
| 7. Round | 19/09/1999 | Dynamo České Budějovice | - | FC Dukla Pribram | 5:0 | ||||
| 8. Round | 26/09/1999 | Dynamo České Budějovice | - | FC Boby-sport Brno | 1:0 | |
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| 9. Round | 02/10/1999 | CU Bohemians Praha | - | Dynamo České Budějovice | 0:1 | |
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| 11. Round | 24/10/1999 | SK Hradec Králové | - | Dynamo České Budějovice | 1:0 | ||||
| 12. Round | 31/10/1999 | Dynamo České Budějovice | - | Slovan Liberec | 0:1 | ||||
| 13. Round | 07/11/1999 | Chmel Blsany | - | Dynamo České Budějovice | 3:2 | ||||
| 14. Round | 21/11/1999 | Dynamo České Budějovice | - | Slavia Praha | 0:1 | ||||
| 15. Round | 26/11/1999 | Sigma Olomouc | - | Dynamo České Budějovice | 1:1 | ||||
| 16. Round | 05/12/1999 | FC Petra Drnovice | - | Dynamo České Budějovice | 2:0 |
Czech Republic