| 1. Round | 18/09/1999 | Panionios GSS | - | Paniliakos Pyrgos | 1:2 | ||||
| 2. Round | 24/09/1999 | Apollon Smyrnis | - | Paniliakos Pyrgos | 0:0 | ||||
| 3. Round | 02/10/1999 | Paniliakos Pyrgos | - | AO Kavala | 2:0 |  |
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| 4. Round | 15/10/1999 | AO Trikala | - | Paniliakos Pyrgos | 1:1 | |
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| 5. Round | 24/10/1999 | Paniliakos Pyrgos | - | AEK Athen | 0:1 | ||||
| 6. Round | 30/10/1999 | PAOK Saloniki | - | Paniliakos Pyrgos | 0:1 | ||||
| 7. Round | 07/11/1999 | Paniliakos Pyrgos | - | Panathinaikos | 0:1 | ||||
| 8. Round | 20/11/1999 | Ethnikos Asteras | - | Paniliakos Pyrgos | 3:1 | ||||
| 9. Round | 27/11/1999 | Paniliakos Pyrgos | - | Iraklis Saloniki | 4:3 | ||||
| 10. Round | 04/12/1999 | Paniliakos Pyrgos | - | PS Kalamata | 3:1 | ||||
| 11. Round | 11/12/1999 | Olympiakos Piraeus | - | Paniliakos Pyrgos | 2:1 | ||||
| 12. Round | 21/12/1999 | Paniliakos Pyrgos | - | Ionikos Nikea | 3:0 | ||||
| 13. Round | 29/12/1999 | Aris Saloniki | - | Paniliakos Pyrgos | 2:1 | ||||
| 14. Round | 08/01/2000 | Paniliakos Pyrgos | - | OFI Heraklion | 1:2 |
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