| 2. Round | 21/08/2016 | Bangor City | - | Connah's Quay Nomads | 0:2 | ||||
| 5. Round | 03/09/2016 | Connah's Quay Nomads | - | Bala Town | 1:1 | ||||
| 6. Round | 11/09/2016 | Cardiff Metropolitan | - | Connah's Quay Nomads | 1:2 | ||||
| 7. Round | 18/09/2016 | Connah's Quay Nomads | - | Aberystwyth Town | 4:0 | ||||
| 8. Round | 20/09/2016 | Connah's Quay Nomads | - | Llandudno FC | 1:1 | ||||
| 9. Round | 25/09/2016 | Connah's Quay Nomads | - | Rhyl FC | 2:0 | ||||
| 10. Round | 02/10/2016 | Connah's Quay Nomads | - | Carmarthen Town | 1:0 | ||||
| 12. Round | 16/10/2016 | Connah's Quay Nomads | - | Bangor City | 2:2 | ||||
| 14. Round | 30/10/2016 | The New Saints | - | Connah's Quay Nomads | 3:0 | ||||
| 11. Round | 13/11/2016 | Llandudno FC | - | Connah's Quay Nomads | 0:2 | ||||
| 17. Round | 25/11/2016 | Rhyl FC | - | Connah's Quay Nomads | 1:2 |  |
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| 18. Round | 13/12/2016 | Connah's Quay Nomads | - | Cefn Druids | 1:0 | ||||
| 19. Round | 17/12/2016 | Connah's Quay Nomads | - | The New Saints | 0:3 | ||||
| 20. Round | 26/12/2016 | Airbus UK | - | Connah's Quay Nomads | 0:3 | ||||
| 21. Round | 30/12/2016 | Connah's Quay Nomads | - | Airbus UK | 5:1 | ||||
| 22. Round | 14/01/2017 | Bala Town | - | Connah's Quay Nomads | 0:0 |
England