| 1. Jornada | 28.02.1999 | Yverdon Sport FC | - | FC Aarau | 2:1 | ||||
| 2. Jornada | 07.03.1999 | FC Aarau | - | FC Lugano | 0:1 | ||||
| 3. Jornada | 14.03.1999 | FC Sion | - | FC Aarau | 1:1 | ||||
| 4. Jornada | 21.03.1999 | FC Aarau | - | FC Wil 1900 | 3:1 |  |
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| 6. Jornada | 10.04.1999 | Etoile Carouge FC | - | FC Aarau | 3:1 | ||||
| 7. Jornada | 17.04.1999 | FC Aarau | - | BSC Young Boys | 1:1 | ||||
| 8. Jornada | 24.04.1999 | BSC Young Boys | - | FC Aarau | 4:1 | ||||
| 9. Jornada | 01.05.1999 | FC Aarau | - | Etoile Carouge FC | 3:1 | ||||
| 10. Jornada | 09.05.1999 | SR Delémont | - | FC Aarau | 2:1 | ||||
| 11. Jornada | 16.05.1999 | FC Wil 1900 | - | FC Aarau | 2:3 | |
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| 12. Jornada | 22.05.1999 | FC Aarau | - | FC Sion | 4:1 | ||||
| 13. Jornada | 29.05.1999 | FC Lugano | - | FC Aarau | 1:2 | |
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| 14. Jornada | 05.06.1999 | FC Aarau | - | Yverdon Sport FC | 2:1 | |
Bulgaria