| 1. Round | 19/09/1999 | Panathinaikos | - | AO Trikala | 2:0 |  |
|||
| 2. Round | 25/09/1999 | AEK Athen | - | Panathinaikos | 1:2 | |
|||
| 3. Round | 02/10/1999 | Panathinaikos | - | PAOK Saloniki | 1:1 | ||||
| 4. Round | 16/10/1999 | Panathinaikos | - | PS Kalamata | 5:0 | |
|||
| 5. Round | 24/10/1999 | Ethnikos Asteras | - | Panathinaikos | 1:2 | ||||
| 6. Round | 30/10/1999 | Panathinaikos | - | Iraklis Saloniki | 3:0 | |
|||
| 7. Round | 07/11/1999 | Paniliakos Pyrgos | - | Panathinaikos | 0:1 | ||||
| 8. Round | 20/11/1999 | Panathinaikos | - | Olympiakos Piraeus | 2:0 | ||||
| 9. Round | 28/11/1999 | Ionikos Nikea | - | Panathinaikos | 2:2 | |
 |
||
| 10. Round | 04/12/1999 | Panathinaikos | - | Aris Saloniki | 3:0 | |
Germany