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1/64-finals
1/32-finals
1/16-finals
1/8-finals
Quarter-finals
Semi-finals
Final
Draw
20251/64-finals
1/32-finals
| 1 | Machida | Kyoto Sangyo | 2 : 1 |
| 2 | Vegalta Sendai | Toyama | 0 : 1 |
| 3 | Kyoto | Nara Club | 1 : 0 |
| 4 | Yokohama FC | Grulla Morioka | 2 : 1 |
| 5 | Kashima Antlers | Kusatsu | 4 : 0 |
| 6 | V-Varen Nagasaki | Tsukuba Univ. | 2 : 1 |
| 7 | Avispa Fukuoka | Okinawa SV | 2 : 0 |
| 8 | Okayama | Giravanz Kitakyushu | 0 : 2 |
| 9 | FC Tokyo | Kanazawa | 3 : 1 |
| 10 | Hokkaido Consadole Sapporo | Oita Trinita | 2 : 3 |
| 11 | Cerezo Osaka | Wakayama | 5 : 0 |
| 12 | Tokushima | Renofa Yamaguchi | 2 : 1 |
| 13 | Gamba Osaka | Veertien Mie | 2 : 1 |
| 14 | Montedio Yamagata | Kagoshima Utd | 2 : 1 |
| 16 | Bye | Urawa Reds | |
| 17 | Kawasaki Frontale | Fukushima Utd | 4 : 3 |
| 18 | Iwata | Sagamihara | 1 : 2 |
| 19 | Yokohama F. Marinos | Reinmeer Aomori | 0 : 2 |
| 20 | Iwaki | Blaublitz | 1 : 2 |
| 21 | Vissel Kobe | Kochi United | 4 : 1 |
| 22 | Kofu | Fukui Utd. | 2 : 1 |
| 23 | Albirex Niigata | Fukuyama City | 1 : 0 |
| 24 | Kashiwa Reysol | Toyo University | 0 : 2 |
| 25 | Verdy | Tochigi SC | 3 : 1 |
| 26 | Sagan Tosu | Ehime | 1 : 0 |
| 27 | Nagoya Grampus | Veroskronos Tsuno | 3 : 0 |
| 28 | Chiba | Kumamoto | 1 : 2 |
| 29 | Sanfrecce Hiroshima | Brew Saga | 3 : 1 |
| 30 | Fujieda MYFC | Baleine Shimonoseki | 2 : 0 |
| 31 | Shonan Bellmare | Gifu | 2 : 0 |
| 32 | Shimizu S-Pulse | Yamaga | 4 : 2 |
1/16-finals
| 1 | Machida | Toyama | 2 : 1 |
| 2 | Kyoto | Yokohama FC | 4 : 3 |
| 3 | Kashima Antlers | V-Varen Nagasaki | 2 : 1 |
| 4 | Avispa Fukuoka | Giravanz Kitakyushu | 1 : 0 |
| 5 | FC Tokyo | Oita Trinita | 2 : 0 |
| 6 | Cerezo Osaka | Tokushima | 2 : 0 |
| 7 | Gamba Osaka | Montedio Yamagata | 4 : 5 |
| 8 | Bye | Urawa Reds | |
| 9 | Kawasaki Frontale | Sagamihara | 0 : 1 |
| 10 | Reinmeer Aomori | Blaublitz | 1 : 2 |
| 11 | Vissel Kobe | Kofu | 2 : 1 |
| 12 | Albirex Niigata | Toyo University | 1 : 2 |
| 13 | Verdy | Sagan Tosu | 1 : 0 |
| 14 | Nagoya Grampus | Kumamoto | 2 : 1 |
| 15 | Sanfrecce Hiroshima | Fujieda MYFC | 5 : 2 |
| 16 | Shonan Bellmare | Shimizu S-Pulse | 0 : 1 |
1/8-finals
| 1 | Machida | Kyoto | 1 : 0 |
| 2 | Kashima Antlers | Avispa Fukuoka | 3 : 2 |
| 3 | FC Tokyo | Cerezo Osaka | 2 : 1 |
| 4 | Montedio Yamagata | Urawa Reds | 1 : 2 |
| 5 | Sagamihara | Blaublitz | 2 : 1 |
| 6 | Vissel Kobe | Toyo University | 2 : 1 |
| 7 | Verdy | Nagoya Grampus | 1 : 2 |
| 8 | Sanfrecce Hiroshima | Shimizu S-Pulse | 3 : 0 |
Quarter-finals
| 1 | Machida | Kashima Antlers | 3 : 0 |
| 2 | FC Tokyo | Urawa Reds | 2 : 1 |
| 3 | Sagamihara | Vissel Kobe | 1 : 2 |
| 4 | Nagoya Grampus | Sanfrecce Hiroshima | 2 : 4 |
Semi-finals
| 1 | Machida | FC Tokyo | 2 : 0 |
| 2 | Vissel Kobe | Sanfrecce Hiroshima | 2 : 0 |
Final
| 1 | Machida | Vissel Kobe | 3 : 1 |
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