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1/32-finals
1/16-finals
1/8-finals
Quarter-finals
Semi-finals
Final
2012
1/32-finals
| 1 | Gamba Osaka | Kansai | 3 : 0 |
| 2 | Oita Trinita | Mito | 2 : 3 |
| 3 | Imabari | Sanfrecce Hiroshima | 2 : 1 |
| 4 | Giravanz Kitakyushu | Machida | 1 : 2 |
| 5 | Shimizu S-Pulse | Wakayama | 5 : 0 |
| 6 | Verspah Oita | Verdy | 0 : 3 |
| 7 | Montedio Yamagata | Tonan Maebashi | 3 : 0 |
| 8 | Nara Club | Cerezo Osaka | 0 : 4 |
| 9 | Chiba | V-Varen Nagasaki | 1 : 0 |
| 10 | Vissel Kobe | Sagawa Shiga | 1 : 2 |
| 11 | Albirex Niigata | Saurcos Fukui | 2 : 1 |
| 12 | Kofu | Fukushima Utd | 0 : 1 |
| 13 | Iwata | Suzuka Rampole | 7 : 0 |
| 14 | Yamaga | Kyoto | 1 : 3 |
| 15 | Gainare Tottori | Kusatsu | 2 : 1 |
| 16 | Tsukuba Univ. | Kashima Antlers | 0 : 2 |
| 17 | Yokohama F. Marinos | YSCC | 1 : 0 |
| 18 | Tochigi SC | Yokohama FC | 0 : 1 |
| 19 | Kamatamare | Sagan Tosu | 1 : 0 |
| 20 | Volca Kagoshima | Urawa Reds | 1 : 2 |
| 21 | Kumamoto | Gifu | 4 : 3 |
| 22 | Sony Sendai | Vegalta Sendai | 0 : 1 |
| 23 | Okayama | Toyama | 2 : 0 |
| 24 | Kariya | Nagoya Grampus | 0 : 2 |
| 25 | Omiya Ardija | Blaublitz | 2 : 0 |
| 26 | Fukuoka Univ. | Avispa Fukuoka | 2 : 4 |
| 27 | Tokushima | Okayama II | 5 : 1 |
| 28 | Tokuyama | Kawasaki Frontale | 0 : 2 |
| 29 | Yokogawa | FC Tokyo | 1 : 0 |
| 30 | Hokkaido Consadole Sapporo | Nagano | 1 : 2 |
| 31 | Shonan Bellmare | Ehime | 1 : 0 |
| 32 | Kashiwa Reysol U18 | Kashiwa Reysol | 0 : 3 |
1/16-finals
| 1 | Gamba Osaka | Mito | 1 : 0 |
| 2 | Imabari | Machida | 2 : 5 |
| 3 | Shimizu S-Pulse | Verdy | 1 : 0 |
| 4 | Montedio Yamagata | Cerezo Osaka | 1 : 2 |
| 5 | Chiba | Sagawa Shiga | 2 : 1 |
| 6 | Albirex Niigata | Fukushima Utd | 0 : 1 |
| 7 | Iwata | Kyoto | 2 : 1 |
| 8 | Gainare Tottori | Kashima Antlers | 1 : 2 |
| 9 | Yokohama F. Marinos | Yokohama FC | 2 : 1 |
| 10 | Kamatamare | Urawa Reds | 1 : 2 |
| 11 | Kumamoto | Vegalta Sendai | 2 : 1 |
| 12 | Okayama | Nagoya Grampus | 2 : 3 |
| 13 | Omiya Ardija | Avispa Fukuoka | 3 : 1 |
| 14 | Tokushima | Kawasaki Frontale | 2 : 3 |
| 15 | Yokogawa | Nagano | 1 : 0 |
| 16 | Shonan Bellmare | Kashiwa Reysol | 1 : 2 |
1/8-finals
| 1 | Gamba Osaka | Machida | 3 : 2 |
| 2 | Shimizu S-Pulse | Cerezo Osaka | 0 : 4 |
| 3 | Chiba | Fukushima Utd | 5 : 0 |
| 4 | Iwata | Kashima Antlers | 1 : 3 |
| 5 | Yokohama F. Marinos | Urawa Reds | 2 : 0 |
| 6 | Kumamoto | Nagoya Grampus | 2 : 5 |
| 7 | Omiya Ardija | Kawasaki Frontale | 4 : 3 |
| 8 | Yokogawa | Kashiwa Reysol | 0 : 1 |
Quarter-finals
| 1 | Gamba Osaka | Cerezo Osaka | 2 : 1 |
| 2 | Chiba | Kashima Antlers | 0 : 1 |
| 3 | Yokohama F. Marinos | Nagoya Grampus | 1 : 0 |
| 4 | Omiya Ardija | Kashiwa Reysol | 2 : 3 |
Semi-finals
| 1 | Gamba Osaka | Kashima Antlers | 1 : 0 |
| 2 | Yokohama F. Marinos | Kashiwa Reysol | 0 : 1 |
Final
| 1 | Gamba Osaka | Kashiwa Reysol | 0 : 1 |
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