| 3. Round | 24/07/2021 | Fakel Voronezh | - | FK Tom Tomsk | 2:0 |  |
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| 4. Round | 31/07/2021 | Veles Moskva | - | FK Tom Tomsk | 1:0 | ||||
| 5. Round | 08/08/2021 | FK Tom Tomsk | - | FK Orenburg | 1:2 | ||||
| 10. Round | 11/09/2021 | FK Krasnodar 2 | - | FK Tom Tomsk | 2:1 | ||||
| 11. Round | 15/09/2021 | Torpedo Moskva | - | FK Tom Tomsk | 3:3 | ||||
| 14. Round | 29/09/2021 | Spartak Moskva 2 | - | FK Tom Tomsk | 3:1 | ||||
| 15. Round | 03/10/2021 | FK Tom Tomsk | - | Alania Vladikavkaz | 1:3 | ||||
| 17. Round | 13/10/2021 | FK Tom Tomsk | - | Olimp-Dolgoprudny | 1:1 | ||||
| 20. Round | 31/10/2021 | Baltika Kaliningrad | - | FK Tom Tomsk | 4:0 | ||||
| 21. Round | 06/11/2021 | FK Tom Tomsk | - | Fakel Voronezh | 2:2 | ||||
| 22. Round | 13/11/2021 | FK Tom Tomsk | - | Veles Moskva | 1:0 | |
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| 23. Round | 17/11/2021 | FK Orenburg | - | FK Tom Tomsk | 2:1 | ||||
| 24. Round | 21/11/2021 | Akron Tolyatti | - | FK Tom Tomsk | 3:3 | ||||
| 25. Round | 27/11/2021 | FK Tom Tomsk | - | FK Neftekhimik | 1:1 |
Russia