| 2. Round | 24/09/1999 | Apollon Smyrnis | - | Paniliakos Pyrgos | 0:0 | ||||
| 9. Round | 27/11/1999 | Paniliakos Pyrgos | - | Iraklis Saloniki | 4:3 |  |
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| 10. Round | 04/12/1999 | Paniliakos Pyrgos | - | PS Kalamata | 3:1 | ||||
| 28. Round | 15/04/2000 | Paniliakos Pyrgos | - | Olympiakos Piraeus | 0:3 | ||||
| 30. Round | 02/05/2000 | Paniliakos Pyrgos | - | Aris Saloniki | 1:2 | ||||
| 31. Round | 06/05/2000 | OFI Heraklion | - | Paniliakos Pyrgos | 3:2 | ||||
| 32. Round | 13/05/2000 | Paniliakos Pyrgos | - | Skoda Xanthi | 2:0 | ||||
| 33. Round | 20/05/2000 | Panachaiki GE | - | Paniliakos Pyrgos | 2:0 |  |
Greece