| 9. Round | 27/10/2012 | FC Carl Zeiss Jena [Youth] | - | Rot-Weiß Erfurt [Youth] | 2:1 | ||||
| 10. Round | 03/11/2012 | VfL Osnabrück [Youth] | - | FC Carl Zeiss Jena [Youth] | 2:0 |  |
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| 11. Round | 10/11/2012 | FC Carl Zeiss Jena [Youth] | - | VfL Wolfsburg [Youth] | 1:3 | ||||
| 12. Round | 24/11/2012 | Hansa Rostock [Youth] | - | FC Carl Zeiss Jena [Youth] | 1:0 | ||||
| 13. Round | 01/12/2012 | FC Carl Zeiss Jena [Youth] | - | Energie Cottbus [Youth] | 1:3 | ||||
| 16. Round | 10/02/2013 | FC Carl Zeiss Jena [Youth] | - | Hamburger SV [Youth] | 1:0 |  |
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| 19. Round | 02/03/2013 | Chemnitzer FC [Youth] | - | FC Carl Zeiss Jena [Youth] | 1:3 | |
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| 20. Round | 17/03/2013 | Hallescher FC [Youth] | - | FC Carl Zeiss Jena [Youth] | 0:2 | ||||
| 21. Round | 07/04/2013 | FC Carl Zeiss Jena [Youth] | - | Werder Bremen [Youth] | 2:1 | |
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| 22. Round | 12/04/2013 | Rot-Weiß Erfurt [Youth] | - | FC Carl Zeiss Jena [Youth] | 2:1 |  |
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| 23. Round | 20/04/2013 | FC Carl Zeiss Jena [Youth] | - | VfL Osnabrück [Youth] | 1:2 | |
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| 25. Round | 05/05/2013 | FC Carl Zeiss Jena [Youth] | - | Hansa Rostock [Youth] | 1:3 | |
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| 26. Round | 12/05/2013 | Energie Cottbus [Youth] | - | FC Carl Zeiss Jena [Youth] | 0:4 |
Germany