| 3. Jornada | 10.09.2016 | Levadiakos | - | Panathinaikos | 0:3 |  |
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| 4. Jornada | 18.09.2016 | Panathinaikos | - | PAS Giannina | 4:0 | |
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| 7. Jornada | 16.10.2016 | Panathinaikos | - | Xanthi FC | 1:2 | |
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| 9. Jornada | 30.10.2016 | Panathinaikos | - | AEP Iraklis FC | 2:0 | |
 |
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| 10. Jornada | 06.11.2016 | Olympiacos | - | Panathinaikos | 3:0 | ||||
| 13. Jornada | 04.12.2016 | Panathinaikos | - | PAOK Saloniki | 1:0 | |
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| 15. Jornada | 18.12.2016 | AE Lárissa | - | Panathinaikos | 0:0 | |
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| 1. Jornada | 05.01.2017 | Platanias Chanion | - | Panathinaikos | 1:0 | ||||
| 2. Jornada | 09.01.2017 | Panathinaikos | - | AO Kerkyra | 1:0 | |
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| 11. Jornada | 15.01.2017 | Panathinaikos | - | AEK Athen | 0:0 | |
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| 16. Jornada | 19.01.2017 | Panathinaikos | - | Platanias Chanion | 2:1 | ||||
| 17. Jornada | 22.01.2017 | AO Kerkyra | - | Panathinaikos | 1:1 | ||||
| 23. Jornada | 04.03.2017 | Panathinaikos | - | Veria FC | 5:0 | ||||
| 24. Jornada | 11.03.2017 | AEP Iraklis FC | - | Panathinaikos | 1:1 | ||||
| 25. Jornada | 19.03.2017 | Panathinaikos | - | Olympiacos | 1:0 | ||||
| 26. Jornada | 02.04.2017 | AEK Athen | - | Panathinaikos | 2:3 | |
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| 27. Jornada | 06.04.2017 | Panathinaikos | - | Panionios GSS | 1:0 | ||||
| 30. Jornada | 30.04.2017 | Panathinaikos | - | AE Lárissa | 2:0 | |
Argentina