| 3. Round | 23/07/2016 | Volgar Astrakhan | - | Shinnik Yaroslavl | 2:0 | ||||
| 5. Round | 31/07/2016 | Shinnik Yaroslavl | - | Luch-Energiya Vladivostok | 3:1 | ||||
| 6. Round | 06/08/2016 | Shinnik Yaroslavl | - | Spartak Moskva 2 | 4:0 | ||||
| 18. Round | 22/10/2016 | Enisey Krasnoyarsk | - | Shinnik Yaroslavl | 1:3 | ||||
| 19. Round | 30/10/2016 | Shinnik Yaroslavl | - | Dinamo Moskva | 2:3 |  |
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| 20. Round | 05/11/2016 | Zenit St. Petersburg 2 | - | Shinnik Yaroslavl | 1:1 | ||||
| 31. Round | 12/04/2017 | Shinnik Yaroslavl | - | Kuban Krasnodar (1928-2018) | 0:1 | ||||
| 34. Round | 29/04/2017 | Shinnik Yaroslavl | - | FK Neftekhimik | 2:1 | ||||
| 37. Round | 14/05/2017 | Dinamo Moskva | - | Shinnik Yaroslavl | 1:0 | |
Russia