| 3. Round | 14/08/2016 | KV Oostende | - | Royal Excel Mouscron | 2:1 | ||||
| 4. Round | 20/08/2016 | Royal Excel Mouscron | - | Sint-Truidense VV | 2:1 | ||||
| 5. Round | 27/08/2016 | Sporting Lokeren | - | Royal Excel Mouscron | 2:1 | ||||
| 11. Round | 22/10/2016 | KV Mechelen | - | Royal Excel Mouscron | 2:0 | ||||
| 12. Round | 27/10/2016 | Waasland-Beveren | - | Royal Excel Mouscron | 0:0 |  |
|||
| 13. Round | 30/10/2016 | Royal Excel Mouscron | - | KV Kortrijk | 0:1 | ||||
| 18. Round | 10/12/2016 | Royal Excel Mouscron | - | KV Mechelen | 1:4 | ||||
| 19. Round | 17/12/2016 | Sporting Charleroi | - | Royal Excel Mouscron | 2:0 | ||||
| 20. Round | 20/12/2016 | Royal Excel Mouscron | - | KVC Westerlo | 0:0 | ||||
| 21. Round | 26/12/2016 | Club Brugge KV | - | Royal Excel Mouscron | 2:1 | ||||
| 23. Round | 24/01/2017 | SV Zulte Waregem | - | Royal Excel Mouscron | 1:0 |
Serbia