| 4. Round | 21/08/2016 | Spartak Moskva | - | FK Krasnodar | 2:0 | ||||
| 5. Round | 28/08/2016 | FK Krasnodar | - | Lokomotiv Moskva | 1:2 | ||||
| 8. Round | 24/09/2016 | CSKA Moskva | - | FK Krasnodar | 1:1 | ||||
| 10. Round | 16/10/2016 | Arsenal Tula | - | FK Krasnodar | 0:0 | ||||
| 12. Round | 30/10/2016 | Anzhi Makhachkala | - | FK Krasnodar | 0:0 | ||||
| 14. Round | 20/11/2016 | FK Krasnodar | - | FK Ural | 3:0 | ||||
| 15. Round | 27/11/2016 | FK Krasnodar | - | Zenit St. Petersburg | 2:1 | ||||
| 16. Round | 01/12/2016 | Terek Grozny | - | FK Krasnodar | 2:1 |  |
Russia