| 3. Round | 10/09/2016 | Panionios GSS | - | Asteras Tripolis | 3:0 | ||||
| 4. Round | 17/09/2016 | Xanthi FC | - | Panionios GSS | 0:2 | ||||
| 5. Round | 24/09/2016 | Panionios GSS | - | Veria FC | 1:2 |  |
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| 6. Round | 01/10/2016 | AEP Iraklis FC | - | Panionios GSS | 1:2 | ||||
| 7. Round | 15/10/2016 | Panionios GSS | - | Olympiakos Piraeus | 0:2 | ||||
| 8. Round | 22/10/2016 | AEK Athen | - | Panionios GSS | 0:0 | |
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| 9. Round | 29/10/2016 | AE Lárissa | - | Panionios GSS | 2:0 | ||||
| 10. Round | 06/11/2016 | Panionios GSS | - | PAOK Saloniki | 1:0 | ||||
| 12. Round | 27/11/2016 | Panionios GSS | - | Panathinaikos | 1:1 | ||||
| 13. Round | 03/12/2016 | Platanias Chanion | - | Panionios GSS | 1:1 | ||||
| 14. Round | 11/12/2016 | Panionios GSS | - | AO Kerkyra | 1:0 | ||||
| 11. Round | 15/01/2017 | Atromitos | - | Panionios GSS | 1:2 | ||||
| 28. Round | 09/04/2017 | Panionios GSS | - | Platanias Chanion | 1:1 |
France
Cameroon 
