| 23. Round | 27/02/1988 | SpVgg Bayreuth | - | FC St. Pauli | 1:3 |  |
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| 26. Round | 19/03/1988 | FC St. Pauli | - | Fortuna Köln | 5:1 | ||||
| 30. Round | 09/04/1988 | FC St. Pauli | - | SV Meppen | 2:0 | ||||
| 31. Round | 16/04/1988 | Arminia Bielefeld | - | FC St. Pauli | 0:1 | ||||
| 32. Round | 23/04/1988 | FC St. Pauli | - | SG Wattenscheid 09 | 3:1 | ||||
| 34. Round | 07/05/1988 | FC St. Pauli | - | Stuttgarter Kickers | 0:2 | |
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| 35. Round | 14/05/1988 | SC Freiburg | - | FC St. Pauli | 1:1 | ||||
| 36. Round | 18/05/1988 | Blau-Weiß 90 Berlin | - | FC St. Pauli | 2:2 | ||||
| 37. Round | 24/05/1988 | FC St. Pauli | - | Rot-Weiß Oberhausen | 2:0 | ||||
| 38. Round | 29/05/1988 | SSV Ulm 1846 | - | FC St. Pauli | 0:1 |
Germany