| 1. Round | 07/07/1999 | Neuchâtel Xamax FC | - | FC Aarau | 1:1 | ||||
| 2. Round | 14/07/1999 | FC Basel 1893 | - | Neuchâtel Xamax FC | 1:1 |  |
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| 3. Round | 17/07/1999 | Neuchâtel Xamax FC | - | FC Lugano | 3:1 | ||||
| 4. Round | 21/07/1999 | Neuchâtel Xamax FC | - | Yverdon Sport FC | 1:1 |  |
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| 6. Round | 31/07/1999 | Neuchâtel Xamax FC | - | FC St. Gallen | 2:2 | ||||
| 7. Round | 07/08/1999 | SR Delémont | - | Neuchâtel Xamax FC | 2:2 | ||||
| 8. Round | 14/08/1999 | Neuchâtel Xamax FC | - | Servette FC | 3:2 | ||||
| 12. Round | 18/09/1999 | FC Aarau | - | Neuchâtel Xamax FC | 4:1 | ||||
| 13. Round | 23/09/1999 | Neuchâtel Xamax FC | - | FC Basel 1893 | 1:2 | ||||
| 17. Round | 31/10/1999 | FC St. Gallen | - | Neuchâtel Xamax FC | 2:1 | ||||
| 18. Round | 06/11/1999 | Neuchâtel Xamax FC | - | SR Delémont | 2:0 | |
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| 19. Round | 20/11/1999 | Servette FC | - | Neuchâtel Xamax FC | 2:4 |  |
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| 21. Round | 05/12/1999 | Lausanne Sports | - | Neuchâtel Xamax FC | 0:2 | ||||
| 22. Round | 12/12/1999 | Neuchâtel Xamax FC | - | FC Zürich | 3:0 dec. |
France