| 2. Round | 08/08/2016 | FK Krasnodar | - | Terek Grozny | 4:0 |  |
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| 3. Round | 13/08/2016 | Krylia Sovetov | - | FK Krasnodar | 1:1 | ||||
| 13. Round | 06/11/2016 | FK Krasnodar | - | FK Orenburg | 3:3 | ||||
| 16. Round | 01/12/2016 | Terek Grozny | - | FK Krasnodar | 2:1 | ||||
| 18. Round | 05/03/2017 | FK Krasnodar | - | Spartak Moskva | 2:2 | ||||
| 19. Round | 13/03/2017 | Lokomotiv Moskva | - | FK Krasnodar | 1:2 | |
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| 20. Round | 19/03/2017 | FK Krasnodar | - | FK Ufa | 0:0 | ||||
| 24. Round | 23/04/2017 | FK Krasnodar | - | Arsenal Tula | 2:0 | ||||
| 25. Round | 27/04/2017 | FK Amkar Perm | - | FK Krasnodar | 0:2 | |
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| 26. Round | 01/05/2017 | FK Krasnodar | - | Anzhi Makhachkala | 0:0 | ||||
| 27. Round | 07/05/2017 | FK Orenburg | - | FK Krasnodar | 1:0 |  |
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| 28. Round | 13/05/2017 | FK Ural | - | FK Krasnodar | 1:1 | ||||
| 29. Round | 17/05/2017 | Zenit St. Petersburg | - | FK Krasnodar | 1:0 | ||||
| 30. Round | 21/05/2017 | FK Tom Tomsk | - | FK Krasnodar | 1:5 |
Brazil