| 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 | ||||
| 17. Round | 24/10/2020 | Veles Moskva | - | FK Tom Tomsk | 0:0 |  |
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| 18. Round | 28/10/2020 | FK Tom Tomsk | - | SKA-Khabarovsk | 1:2 | ||||
| 19. Round | 01/11/2020 | FK Chayka | - | FK Tom Tomsk | 1:1 | ||||
| 32. Round | 24/03/2021 | Shinnik Yaroslavl | - | FK Tom Tomsk | 2:3 | ||||
| 33. Round | 28/03/2021 | FK Tom Tomsk | - | Torpedo Moskva | 1:0 | ||||
| 34. Round | 03/04/2021 | Akron Tolyatti | - | FK Tom Tomsk | 0:0 | ||||
| 35. Round | 07/04/2021 | FK Tom Tomsk | - | FK Krasnodar 2 | 1:1 | ||||
| 36. Round | 11/04/2021 | Baltika Kaliningrad | - | FK Tom Tomsk | 0:1 | ||||
| 37. Round | 17/04/2021 | FK Tom Tomsk | - | Veles Moskva | 0:0 | ||||
| 38. Round | 24/04/2021 | SKA-Khabarovsk | - | FK Tom Tomsk | 1:1 | |
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| 39. Round | 28/04/2021 | FK Tom Tomsk | - | FK Chayka | 3:0 | ||||
| 40. Round | 02/05/2021 | FK Orenburg | - | FK Tom Tomsk | 2:0 | ||||
| 41. Round | 08/05/2021 | FK Tom Tomsk | - | Enisey Krasnoyarsk | 1:0 | ||||
| 42. Round | 15/05/2021 | FK Tom Tomsk | - | FK Nizhny Novgorod | 1:1 |
Russia