| 1. Jornada | 01.08.2016 | FK Krasnodar | - | FK Tom Tomsk | 3:0 | ||||
| 2. Jornada | 07.08.2016 | Lokomotiv Moskva | - | FK Tom Tomsk | 2:2 |  |
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| 3. Jornada | 14.08.2016 | FK Tom Tomsk | - | FK Ufa | 1:0 |  |
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| 4. Jornada | 20.08.2016 | FK Rostov | - | FK Tom Tomsk | 3:0 | ||||
| 5. Jornada | 27.08.2016 | FK Tom Tomsk | - | CSKA Moscú | 0:1 | ||||
| 6. Jornada | 10.09.2016 | FK Amkar Perm | - | FK Tom Tomsk | 1:0 | ||||
| 7. Jornada | 17.09.2016 | FK Tom Tomsk | - | Arsenal Tula | 1:0 | ||||
| 8. Jornada | 26.09.2016 | Rubin Kazan | - | FK Tom Tomsk | 2:1 | ||||
| 9. Jornada | 01.10.2016 | FK Tom Tomsk | - | FK Ural | 1:1 | ||||
| 11. Jornada | 22.10.2016 | FK Tom Tomsk | - | Anzhi Makhachkala | 0:3 | ||||
| 14. Jornada | 21.11.2016 | Terek Grozny | - | FK Tom Tomsk | 0:0 | |
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| 15. Jornada | 27.11.2016 | Krylia Sovetov | - | FK Tom Tomsk | 3:0 |
Rusia