| 1. Round | 15/03/2004 | Lokomotiv Moskva | - | Shinnik Yaroslavl | 3:0 | ||||
| 2. Round | 21/03/2004 | FK Rostov | - | Shinnik Yaroslavl | 0:0 | ||||
| 3. Round | 28/03/2004 | Shinnik Yaroslavl | - | Kuban Krasnodar (1928-2018) | 1:0 | ||||
| 5. Round | 07/04/2004 | Spartak Moskva | - | Shinnik Yaroslavl | 1:0 | ||||
| 6. Round | 11/04/2004 | Shinnik Yaroslavl | - | Dinamo Moskva | 1:0 | ||||
| 7. Round | 18/04/2004 | Zenit St. Petersburg | - | Shinnik Yaroslavl | 1:0 | ||||
| 9. Round | 01/05/2004 | FK Amkar Perm | - | Shinnik Yaroslavl | 1:1 | ||||
| 10. Round | 08/05/2004 | Shinnik Yaroslavl | - | Rubin Kazan | 1:1 | ||||
| 12. Round | 19/05/2004 | CSKA Moskva | - | Shinnik Yaroslavl | 1:1 | ||||
| 13. Round | 23/05/2004 | Shinnik Yaroslavl | - | FK Saturn | 1:0 | ||||
| 14. Round | 21/07/2004 | FK Moskva | - | Shinnik Yaroslavl | 3:2 |  |
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| 17. Round | 07/08/2004 | Shinnik Yaroslavl | - | FK Moskva | 1:1 | ||||
| 20. Round | 21/08/2004 | Shinnik Yaroslavl | - | FK Amkar Perm | 2:1 | ||||
| 23. Round | 18/09/2004 | Krylia Sovetov | - | Shinnik Yaroslavl | 1:2 |  |
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| 27. Round | 24/10/2004 | Alania Vladikavkaz | - | Shinnik Yaroslavl | 2:1 | ||||
| 30. Round | 12/11/2004 | Shinnik Yaroslavl | - | Lokomotiv Moskva | 0:2 |
Tajikistan