Draw
20251/64-finals
| 1 | Vanraure | Albirex Niigata | 1 : 2 |
| 2 | Yamaga | Sagan Tosu | 1 : 0 |
| 3 | Nagano | Verdy | 0 : 1 |
| 4 | Ehime | Blaublitz | 0 : 2 |
| 5 | Tochigi City | Kashima Antlers | 0 : 1 |
| 6 | Oita Trinita | Renofa Yamaguchi | 2 : 3 |
| 7 | Azul Claro Numazu | Kashiwa Reysol | 0 : 1 |
| 8 | Fukushima Utd | Hokkaido Consadole Sapporo | 6 : 3 |
| 9 | Kanazawa | Shonan Bellmare | 0 : 1 |
| 10 | Kusatsu | V-Varen Nagasaki | 1 : 4 |
| 11 | Nara Club | FC Tokyo | 0 : 1 |
| 12 | Omiya Ardija | Iwaki | 4 : 3 |
| 13 | Sagamihara | Shimizu S-Pulse | 1 : 3 |
| 14 | Osaka | Iwata | 1 : 2 |
| 15 | Kochi United | Gamba Osaka | 1 : 2 |
| 16 | Mito | Kumamoto | 1 : 0 |
| 17 | Gainare Tottori | Kyoto | 0 : 2 |
| 18 | Kagoshima Utd | Montedio Yamagata | 0 : 2 |
| 19 | Kamatamare | Cerezo Osaka | 1 : 5 |
| 20 | Imabari | Tokushima | 2 : 1 |
| 21 | Gifu | Yokohama FC | 0 : 2 |
| 22 | Giravanz Kitakyushu | Okayama | 1 : 0 |
| 23 | Kofu | Fujieda MYFC | 2 : 1 |
| 24 | Bye | Machida | |
| 25 | Tegevajaro Miyazaki | Nagoya Grampus | 0 : 3 |
| 26 | Toyama | Chiba | 4 : 2 |
| 27 | Ryukyu | Avispa Fukuoka | 0 : 2 |
| 28 | Tochigi SC | Vegalta Sendai | 1 : 0 |
| 32 | Bye | Sanfrecce Hiroshima |
1/32-finals
| 1 | Albirex Niigata | Yamaga | 2 : 0 |
| 2 | Verdy | Blaublitz | 2 : 1 |
| 3 | Kashima Antlers | Renofa Yamaguchi | 1 : 2 |
| 4 | Kashiwa Reysol | Fukushima Utd | 3 : 2 |
| 5 | Shonan Bellmare | V-Varen Nagasaki | 2 : 1 |
| 6 | FC Tokyo | Omiya Ardija | 3 : 1 |
| 7 | Shimizu S-Pulse | Iwata | 1 : 2 |
| 8 | Gamba Osaka | Mito | 1 : 0 |
| 9 | Kyoto | Montedio Yamagata | 1 : 0 |
| 10 | Cerezo Osaka | Imabari | 4 : 3 |
| 11 | Yokohama FC | Giravanz Kitakyushu | 2 : 1 |
| 12 | Kofu | Machida | 0 : 1 |
| 13 | Nagoya Grampus | Toyama | 1 : 2 |
| 14 | Avispa Fukuoka | Tochigi SC | 2 : 1 |
| 16 | Bye | Sanfrecce Hiroshima |
1/16-finals
| 1 | Albirex Niigata | Verdy | 0 : 2 |
| 2 | Renofa Yamaguchi | Kashiwa Reysol | 0 : 2 |
| 3 | Shonan Bellmare | FC Tokyo | 1 : 0 |
| 4 | Iwata | Gamba Osaka | 2 : 1 |
| 5 | Kyoto | Cerezo Osaka | 1 : 4 |
| 6 | Yokohama FC | Machida | 2 : 1 |
| 7 | Toyama | Avispa Fukuoka | 1 : 2 |
| 8 | Bye | Sanfrecce Hiroshima |
1/8-finals
| 1 | Verdy | Kashiwa Reysol | |
| 2 | Shonan Bellmare | Iwata | |
| 3 | Cerezo Osaka | Yokohama FC | |
| 4 | Avispa Fukuoka | Sanfrecce Hiroshima |
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