| 10. Round | 29/10/1999 | 1. FC Nürnberg | - | FC St. Pauli | 2:2 | ||||
| 12. Round | 19/11/1999 | Hannover 96 | - | FC St. Pauli | 1:2 | ||||
| 13. Round | 28/11/1999 | FC St. Pauli | - | Karlsruher SC | 3:1 | ||||
| 14. Round | 05/12/1999 | Alemannia Aachen | - | FC St. Pauli | 3:1 | ||||
| 15. Round | 12/12/1999 | FC St. Pauli | - | Energie Cottbus | 1:0 | ||||
| 16. Round | 15/12/1999 | FC St. Pauli | - | 1. FC Köln | 1:2 | ||||
| 20. Round | 25/02/2000 | VfL Bochum | - | FC St. Pauli | 2:0 | ||||
| 24. Round | 24/03/2000 | Kickers Offenbach | - | FC St. Pauli | 0:1 | ||||
| 25. Round | 02/04/2000 | FC St. Pauli | - | Fortuna Köln | 0:0 |  |
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| 26. Round | 07/04/2000 | 1. FSV Mainz 05 | - | FC St. Pauli | 1:1 | ||||
| 27. Round | 14/04/2000 | FC St. Pauli | - | 1. FC Nürnberg | 0:0 | ||||
| 28. Round | 24/04/2000 | Chemnitzer FC | - | FC St. Pauli | 1:3 | ||||
| 29. Round | 28/04/2000 | FC St. Pauli | - | Hannover 96 | 0:2 | ||||
| 30. Round | 05/05/2000 | Karlsruher SC | - | FC St. Pauli | 0:0 | ||||
| 31. Round | 12/05/2000 | FC St. Pauli | - | Alemannia Aachen | 2:1 | ||||
| 32. Round | 18/05/2000 | Energie Cottbus | - | FC St. Pauli | 3:2 | ||||
| 33. Round | 21/05/2000 | 1. FC Köln | - | FC St. Pauli | 6:3 | ||||
| 34. Round | 26/05/2000 | FC St. Pauli | - | Rot-Weiß Oberhausen | 1:1 | |
Germany