| 1. Round | 13/08/2006 | SV Lippstadt 08 | - | FCE Rheine | 3:0 | ||||
| 2. Round | 20/08/2006 | FCE Rheine | - | Hammer SpVg | 0:1 | ||||
| 3. Round | 27/08/2006 | SF Oestrich-Iserlohn | - | FCE Rheine | 2:1 | ||||
| 4. Round | 03/09/2006 | FCE Rheine | - | SpVgg Erkenschwick | 4:1 | ||||
| 5. Round | 10/09/2006 | Arminia Bielefeld II | - | FCE Rheine | 4:2 |  |
|||
| 6. Round | 17/09/2006 | FCE Rheine | - | SV Emsdetten 05 | 0:0 | ||||
| 7. Round | 23/09/2006 | VfL Bochum II | - | FCE Rheine | 4:0 | ||||
| 8. Round | 01/10/2006 | FCE Rheine | - | SC Verl | 1:2 | ||||
| 9. Round | 15/10/2006 | Delbrücker SC | - | FCE Rheine | 0:1 | ||||
| 10. Round | 22/10/2006 | FCE Rheine | - | Rot Weiss Ahlen II | 3:0 | ||||
| 11. Round | 29/10/2006 | Westfalia Herne | - | FCE Rheine | 3:0 | ||||
| 12. Round | 05/11/2006 | FCE Rheine | - | VfB Hüls | 2:0 | ||||
| 13. Round | 10/11/2006 | Preußen Münster | - | FCE Rheine | 1:2 | ||||
| 14. Round | 18/11/2006 | FCE Rheine | - | Sportfreunde Lotte | 2:3 | ||||
| 15. Round | 03/12/2006 | FCE Rheine | - | FC Schalke 04 II | 1:2 | ||||
| 16. Round | 08/12/2006 | SG Wattenscheid 09 | - | FCE Rheine | 1:3 | ||||
| 17. Round | 17/12/2006 | FCE Rheine | - | FC Gütersloh 2000 | 0:0 |
Germany