| 1. Round | 12/08/2000 | LR Ahlen | - | FC St. Pauli | 3:6 | ||||
| 2. Round | 18/08/2000 | FC St. Pauli | - | Waldhof Mannheim | 5:0 | ||||
| 3. Round | 05/09/2000 | SSV Reutlingen | - | FC St. Pauli | 2:0 | ||||
| 4. Round | 10/09/2000 | FC St. Pauli | - | Stuttgarter Kickers | 4:0 | ||||
| 5. Round | 15/09/2000 | MSV Duisburg | - | FC St. Pauli | 4:1 | ||||
| 6. Round | 23/09/2000 | FC St. Pauli | - | Arminia Bielefeld | 2:0 | ||||
| 9. Round | 20/10/2000 | Chemnitzer FC | - | FC St. Pauli | 1:3 | ||||
| 22. Round | 18/02/2001 | FC St. Pauli | - | MSV Duisburg | 1:0 | ||||
| 23. Round | 24/02/2001 | Arminia Bielefeld | - | FC St. Pauli | 3:3 | ||||
| 26. Round | 18/03/2001 | FC St. Pauli | - | Chemnitzer FC | 3:0 | ||||
| 27. Round | 30/03/2001 | 1. FC Saarbrücken | - | FC St. Pauli | 1:0 |  |
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| 28. Round | 08/04/2001 | FC St. Pauli | - | VfL Osnabrück | 2:4 | ||||
| 30. Round | 21/04/2001 | FC St. Pauli | - | Rot-Weiß Oberhausen | 4:1 |
Croatia