| 2. Round | 21/08/2016 | Bangor City | - | Connah's Quay Nomads | 0:2 |  |
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| 3. Round | 28/08/2016 | Connah's Quay Nomads | - | Newtown AFC | 1:0 | ||||
| 4. Round | 31/08/2016 | Cefn Druids | - | Connah's Quay Nomads | 0:0 | ||||
| 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 | ||||
| 13. Round | 23/10/2016 | Connah's Quay Nomads | - | Cardiff Metropolitan | 0:0 | ||||
| 14. Round | 30/10/2016 | The New Saints | - | Connah's Quay Nomads | 3:0 | ||||
| 16. Round | 19/11/2016 | Newtown AFC | - | Connah's Quay Nomads | 2:1 | ||||
| 17. Round | 25/11/2016 | Rhyl FC | - | Connah's Quay Nomads | 1:2 |  |
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| 21. Round | 30/12/2016 | Connah's Quay Nomads | - | Airbus UK | 5:1 | |
England