| 3. Round | 28/08/1999 | NK Istra Pula | - | Hrvatski Dragovoljac | 4:5 |  |
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| 4. Round | 07/09/1999 | Hajduk Split | - | NK Istra Pula | 1:0 | ||||
| 5. Round | 10/09/1999 | NK Istra Pula | - | Croatia Zagreb | 0:4 | ||||
| 6. Round | 18/09/1999 | NK Varteks | - | NK Istra Pula | 4:1 | ||||
| 7. Round | 25/09/1999 | NK Istra Pula | - | HNK Šibenik | 0:0 | ||||
| 8. Round | 02/10/1999 | HNK Rijeka | - | NK Istra Pula | 4:1 | |
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| 9. Round | 12/10/1999 | NK Istra Pula | - | HNK Cibalia | 3:0 | ||||
| 10. Round | 16/10/1999 | NK Istra Pula | - | NK Vukovar 91 | 3:0 | ||||
| 11. Round | 23/10/1999 | NK Zagreb | - | NK Istra Pula | 1:1 | ||||
| 12. Round | 30/10/1999 | Slaven Belupo | - | NK Istra Pula | 1:1 | ||||
| 13. Round | 06/11/1999 | NK Istra Pula | - | NK Osijek | 1:1 | |
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| 14. Round | 23/11/1999 | Hrvatski Dragovoljac | - | NK Istra Pula | 1:0 | ||||
| 15. Round | 27/11/1999 | NK Istra Pula | - | Hajduk Split | 0:5 | ||||
| 16. Round | 04/12/1999 | Croatia Zagreb | - | NK Istra Pula | 3:1 |
Croatia