| 3. Round | 12/09/2016 | AE Lárissa | - | AEP Iraklis FC | 2:2 | ||||
| 4. Round | 18/09/2016 | AEP Iraklis FC | - | Olympiakos Piraeus | 1:2 | ||||
| 5. Round | 26/09/2016 | AEK Athen | - | AEP Iraklis FC | 0:0 |  |
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| 7. Round | 16/10/2016 | PAOK Saloniki | - | AEP Iraklis FC | 1:0 | ||||
| 8. Round | 23/10/2016 | AEP Iraklis FC | - | Atromitos | 1:2 | ||||
| 9. Round | 30/10/2016 | Panathinaikos | - | AEP Iraklis FC | 2:0 | |
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| 10. Round | 07/11/2016 | AEP Iraklis FC | - | Platanias Chanion | 1:1 | |
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| 12. Round | 27/11/2016 | Levadiakos | - | AEP Iraklis FC | 3:0 | ||||
| 13. Round | 05/12/2016 | AEP Iraklis FC | - | PAS Giannina | 2:1 | ||||
| 14. Round | 11/12/2016 | Panetolikos | - | AEP Iraklis FC | 2:0 | ||||
| 1. Round | 03/01/2017 | AEP Iraklis FC | - | Xanthi FC | 0:1 |
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