| 1. Round | 28/07/2000 | SV 07 Elversberg | - | FC Carl Zeiss Jena | 1:0 | ||||
| 2. Round | 05/08/2000 | FC Carl Zeiss Jena | - | SV Darmstadt 98 | 3:2 | ||||
| 5. Round | 26/08/2000 | Eintracht Trier | - | FC Carl Zeiss Jena | 1:1 | ||||
| 6. Round | 01/09/2000 | FC Carl Zeiss Jena | - | Rot-Weiß Erfurt | 0:0 | ||||
| 8. Round | 16/09/2000 | FC Carl Zeiss Jena | - | VfR Mannheim | 0:1 | ||||
| 9. Round | 24/09/2000 | VfB Stuttgart II | - | FC Carl Zeiss Jena | 3:0 |  |
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| 11. Round | 08/10/2000 | 1. FC Schweinfurt 05 | - | FC Carl Zeiss Jena | 3:0 | ||||
| 12. Round | 14/10/2000 | FC Carl Zeiss Jena | - | VfR Aalen | 1:3 | ||||
| 14. Round | 27/10/2000 | FC Carl Zeiss Jena | - | SC Pfullendorf | 1:0 | ||||
| 15. Round | 04/11/2000 | Sportfreunde Siegen | - | FC Carl Zeiss Jena | 1:2 | ||||
| 16. Round | 12/11/2000 | TSV 1860 München II | - | FC Carl Zeiss Jena | 4:0 | ||||
| 19. Round | 03/12/2000 | SV Darmstadt 98 | - | FC Carl Zeiss Jena | 3:1 | ||||
| 20. Round | 09/12/2000 | FC Carl Zeiss Jena | - | Wacker Burghausen | 1:2 | ||||
| 22. Round | 03/03/2001 | FC Carl Zeiss Jena | - | Eintracht Trier | 0:1 | ||||
| 33. Round | 23/05/2001 | FC Carl Zeiss Jena | - | TSV 1860 München II | 1:2 |
Germany