| 6. Round | 06/08/2016 | Baltika Kaliningrad | - | Zenit St. Petersburg 2 | 0:0 | ||||
| 9. Round | 21/08/2016 | Luch-Energiya Vladivostok | - | Baltika Kaliningrad | 1:1 | ||||
| 11. Round | 03/09/2016 | FK Tosno | - | Baltika Kaliningrad | 4:1 | ||||
| 15. Round | 02/10/2016 | Sibir Novosibirsk | - | Baltika Kaliningrad | 1:1 | ||||
| 16. Round | 08/10/2016 | Baltika Kaliningrad | - | Mordovia Saransk | 1:2 | ||||
| 17. Round | 15/10/2016 | Kuban Krasnodar (1928-2018) | - | Baltika Kaliningrad | 1:1 | ||||
| 18. Round | 22/10/2016 | Baltika Kaliningrad | - | Fakel Voronezh | 0:0 | ||||
| 19. Round | 30/10/2016 | Sokol Saratov | - | Baltika Kaliningrad | 1:0 | ||||
| 21. Round | 09/11/2016 | Enisey Krasnoyarsk | - | Baltika Kaliningrad | 2:1 | ||||
| 24. Round | 26/11/2016 | Zenit St. Petersburg 2 | - | Baltika Kaliningrad | 1:1 |  |
Russia