| 1. Round | 01/08/2016 | FK Krasnodar | - | FK Tom Tomsk | 3:0 | ||||
| 6. Round | 11/09/2016 | FK Ufa | - | FK Krasnodar | 0:0 | ||||
| 7. Round | 18/09/2016 | FK Krasnodar | - | FK Rostov | 2:1 | ||||
| 8. Round | 24/09/2016 | CSKA Moskva | - | FK Krasnodar | 1:1 |  |
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| 10. Round | 16/10/2016 | Arsenal Tula | - | FK Krasnodar | 0:0 | ||||
| 12. Round | 30/10/2016 | Anzhi Makhachkala | - | FK Krasnodar | 0:0 | |
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| 13. Round | 06/11/2016 | FK Krasnodar | - | FK Orenburg | 3:3 | ||||
| 15. Round | 27/11/2016 | FK Krasnodar | - | Zenit St. Petersburg | 2:1 | |
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| 20. Round | 19/03/2017 | FK Krasnodar | - | FK Ufa | 0:0 | ||||
| 22. Round | 09/04/2017 | FK Krasnodar | - | CSKA Moskva | 1:1 | ||||
| 26. Round | 01/05/2017 | FK Krasnodar | - | Anzhi Makhachkala | 0:0 | ||||
| 27. Round | 07/05/2017 | FK Orenburg | - | FK Krasnodar | 1:0 | ||||
| 29. Round | 17/05/2017 | Zenit St. Petersburg | - | FK Krasnodar | 1:0 |
Colombia