| 5. Round | 22/08/2020 | FK Tom Tomsk | - | Dinamo Bryansk | 0:2 |  |
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| 7. Round | 05/09/2020 | FK Tom Tomsk | - | Alania Vladikavkaz | 0:1 |  |
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| 8. Round | 09/09/2020 | FK Tom Tomsk | - | Tekstilshchik Ivanovo | 0:2 | ||||
| 9. Round | 13/09/2020 | Krylia Sovetov | - | FK Tom Tomsk | 2:0 | ||||
| 10. Round | 19/09/2020 | FK Tom Tomsk | - | Volgar Astrakhan | 1:3 | |
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| 11. Round | 23/09/2020 | Fakel Voronezh | - | FK Tom Tomsk | 0:0 | |
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| 13. Round | 04/10/2020 | Torpedo Moskva | - | FK Tom Tomsk | 1:0 | ||||
| 14. Round | 09/10/2020 | FK Tom Tomsk | - | Akron Tolyatti | 2:1 | ||||
| 15. Round | 13/10/2020 | FK Krasnodar 2 | - | FK Tom Tomsk | 2:0 | ||||
| 16. Round | 17/10/2020 | FK Tom Tomsk | - | Baltika Kaliningrad | 0:1 | |
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| 18. Round | 28/10/2020 | FK Tom Tomsk | - | SKA-Khabarovsk | 1:2 | |
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| 19. Round | 01/11/2020 | FK Chayka | - | FK Tom Tomsk | 1:1 | ||||
| 22. Round | 15/11/2020 | FK Tom Tomsk | - | FK Chertanovo | 1:2 | |
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| 24. Round | 25/11/2020 | Irtysh Omsk | - | FK Tom Tomsk | 1:0 |
Russia