| 1. Round | 02/07/2016 | Sagan Tosu | - | FC Tokyo | 3:2 | ||||
| 4. Round | 17/07/2016 | FC Tokyo | - | Kashiwa Reysol | 0:1 |  |
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| 5. Round | 23/07/2016 | Kawasaki Frontale | - | FC Tokyo | 1:0 | ||||
| 6. Round | 30/07/2016 | Albirex Niigata | - | FC Tokyo | 0:1 | |
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| 7. Round | 06/08/2016 | FC Tokyo | - | Júbilo Iwata | 3:2 | |
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| 9. Round | 20/08/2016 | FC Tokyo | - | Yokohama F. Marinos | 1:0 | ||||
| 10. Round | 27/08/2016 | Nagoya Grampus | - | FC Tokyo | 1:1 | ||||
| 12. Round | 17/09/2016 | FC Tokyo | - | Urawa Red Diamonds | 1:3 | ||||
| 16. Round | 29/10/2016 | FC Tokyo | - | Vegalta Sendai | 1:0 | ||||
| 17. Round | 03/11/2016 | RB Omiya Ardija | - | FC Tokyo | 0:1 |
Japan