| 1. Round | 17/08/2008 | FC Schalke 04 II | - | Preußen Münster | 1:1 | ||||
| 2. Round | 22/08/2008 | Rot-Weiss Essen | - | FC Schalke 04 II | 4:0 | ||||
| 3. Round | 31/08/2008 | FC Schalke 04 II | - | 1. FSV Mainz 05 II | 1:1 | ||||
| 10. Round | 06/09/2008 | Sportfreunde Lotte | - | FC Schalke 04 II | 0:1 | ||||
| 4. Round | 13/09/2008 | 1. FC Kleve | - | FC Schalke 04 II | 3:2 | ||||
| 5. Round | 21/09/2008 | FC Schalke 04 II | - | Bor. Mönchengladbach II | 1:1 | ||||
| 6. Round | 27/09/2008 | Bayer Leverkusen II | - | FC Schalke 04 II | 0:2 | ||||
| 7. Round | 04/10/2008 | FC Schalke 04 II | - | SV 07 Elversberg | 0:0 | ||||
| 8. Round | 17/10/2008 | FSV Oggersheim | - | FC Schalke 04 II | 0:0 | ||||
| 9. Round | 25/10/2008 | FC Schalke 04 II | - | Borussia Dortmund II | 0:2 | ||||
| 13. Round | 15/11/2008 | VfL Bochum II | - | FC Schalke 04 II | 0:3 |  |
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| 15. Round | 28/11/2008 | Eintracht Trier | - | FC Schalke 04 II | 1:0 | ||||
| 14. Round | 03/12/2008 | FC Schalke 04 II | - | 1. FC Köln II | 3:3 | |
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| 16. Round | 07/12/2008 | FC Schalke 04 II | - | BV Cloppenburg | 1:2 | ||||
| 17. Round | 12/12/2008 | Wormatia Worms | - | FC Schalke 04 II | 0:2 |
Germany