| 25. Jornada | 12.03.2016 | FK Torpedo Armavir | - | FK Tom Tomsk | 1:1 | ||||
| 26. Jornada | 16.03.2016 | Gazovik Orenburg | - | FK Tom Tomsk | 1:0 | ||||
| 27. Jornada | 20.03.2016 | FK Tom Tomsk | - | Shinnik Yaroslavl | 1:1 | ||||
| 28. Jornada | 27.03.2016 | Volgar Astrakhan | - | FK Tom Tomsk | 1:1 | ||||
| 29. Jornada | 03.04.2016 | FK Tom Tomsk | - | Enisey Krasnoyarsk | 2:1 | ||||
| 30. Jornada | 07.04.2016 | FK Tyumen | - | FK Tom Tomsk | 1:1 |  |
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| 31. Jornada | 11.04.2016 | FK Tom Tomsk | - | Luch-Energiya Vladivostok | 0:2 | ||||
| 32. Jornada | 18.04.2016 | SKA-Energiya Khabarovsk | - | FK Tom Tomsk | 1:0 | ||||
| 33. Jornada | 25.04.2016 | FK Tom Tomsk | - | Sokol Saratov | 2:1 | ||||
| 34. Jornada | 02.05.2016 | Volga Nizhniy Novgorod | - | FK Tom Tomsk | 3:2 | ||||
| 36. Jornada | 10.05.2016 | Baltika Kaliningrad | - | FK Tom Tomsk | 0:3 | ||||
| 37. Jornada | 15.05.2016 | FK Tom Tomsk | - | FK Kamaz | 2:0 | ||||
| 38. Jornada | 21.05.2016 | Spartak Moskva 2 | - | FK Tom Tomsk | 0:1 |
Rusia