| 1. Round | 11/07/2016 | FK Tosno | - | FK Khimki | 1:1 | ||||
| 2. Round | 16/07/2016 | FK Khimki | - | FK Tambov | 0:0 | ||||
| 4. Round | 27/07/2016 | FK Neftekhimik | - | FK Khimki | 1:0 | ||||
| 5. Round | 31/07/2016 | FK Khimki | - | Sibir Novosibirsk | 1:1 | ||||
| 7. Round | 13/08/2016 | FK Khimki | - | Kuban Krasnodar (1928-2018) | 4:1 |  |
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| 8. Round | 17/08/2016 | Fakel Voronezh | - | FK Khimki | 2:0 | ||||
| 9. Round | 21/08/2016 | FK Khimki | - | Sokol Saratov | 0:0 | ||||
| 10. Round | 28/08/2016 | Shinnik Yaroslavl | - | FK Khimki | 2:0 | ||||
| 11. Round | 02/09/2016 | FK Khimki | - | FK Tyumen | 3:2 | ||||
| 12. Round | 10/09/2016 | Enisey Krasnoyarsk | - | FK Khimki | 3:0 | ||||
| 14. Round | 26/09/2016 | Baltika Kaliningrad | - | FK Khimki | 0:0 | ||||
| 15. Round | 02/10/2016 | FK Khimki | - | Zenit St. Petersburg 2 | 2:1 |  |
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| 16. Round | 08/10/2016 | Volgar Astrakhan | - | FK Khimki | 1:1 | ||||
| 18. Round | 22/10/2016 | Luch-Energiya Vladivostok | - | FK Khimki | 2:0 |
Russia