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1/32-finals
1/16-finals
1/8-finals
Quarter-finals
Semi-finals
Final
2013
1/32-finals
| 1 | Yokohama F. Marinos | Vanraure | 5 : 1 |
| 2 | Avispa Fukuoka | Tochigi SC | 1 : 5 |
| 3 | Giravanz Kitakyushu | Gainare Tottori | 2 : 0 |
| 4 | Nagoya Grampus | Nagano | 0 : 2 |
| 5 | Kashiwa Reysol | Tsukuba Univ. | 4 : 2 |
| 6 | Gifu | Okayama | 1 : 2 |
| 7 | Albirex Niigata | Niigata University | 4 : 2 |
| 8 | Verspah Oita | Oita Trinita | 0 : 2 |
| 9 | Kawasaki Frontale | Kochi | 3 : 1 |
| 10 | V-Varen Nagasaki | Verdy | 2 : 3 |
| 11 | Urawa Reds | Tochigi Uva | 2 : 1 |
| 12 | Toyama | Montedio Yamagata | 2 : 3 |
| 13 | Cerezo Osaka | Kansai | 4 : 0 |
| 14 | Nara Club | Vissel Kobe | 1 : 3 |
| 15 | Yamaga | Kusatsu | 4 : 3 |
| 16 | Saga University | Sagan Tosu | 0 : 10 |
| 17 | FC Tokyo | Yokogawa | 1 : 0 |
| 18 | Kamatamare | Chiba | 0 : 5 |
| 19 | Gamba Osaka | Imabari | 5 : 0 |
| 20 | Okayama II | Omiya Ardija | 0 : 4 |
| 21 | Shimizu S-Pulse | Fujieda MYFC | 2 : 0 |
| 22 | Yokohama FC | Kanazawa | 0 : 1 |
| 23 | Mito | Ehime | 2 : 1 |
| 24 | Blaublitz | Vegalta Sendai | 0 : 3 |
| 25 | Kofu | Fukushima Utd | 1 : 0 |
| 26 | Ryukyu | Shonan Bellmare | 0 : 4 |
| 27 | Iwata | Saurcos Fukui | 8 : 1 |
| 28 | Hokkaido University | Hokkaido Consadole Sapporo | 1 : 4 |
| 29 | Kashima Antlers | Sony Sendai | 3 : 0 |
| 30 | Sagawa Printing | Kyoto | 0 : 4 |
| 31 | Kumamoto | Tokushima | 2 : 1 |
| 32 | Fukuoka Univ. | Sanfrecce Hiroshima | 0 : 1 |
1/16-finals
| 1 | Yokohama F. Marinos | Tochigi SC | 3 : 1 |
| 2 | Giravanz Kitakyushu | Nagano | 0 : 1 |
| 3 | Kashiwa Reysol | Okayama | 1 : 0 |
| 4 | Albirex Niigata | Oita Trinita | 0 : 1 |
| 5 | Kawasaki Frontale | Verdy | 3 : 0 |
| 6 | Urawa Reds | Montedio Yamagata | 2 : 3 |
| 7 | Cerezo Osaka | Vissel Kobe | 4 : 0 |
| 8 | Yamaga | Sagan Tosu | 1 : 3 |
| 9 | FC Tokyo | Chiba | 2 : 1 |
| 10 | Gamba Osaka | Omiya Ardija | 0 : 1 |
| 11 | Shimizu S-Pulse | Kanazawa | 3 : 2 |
| 12 | Mito | Vegalta Sendai | 1 : 2 |
| 13 | Kofu | Shonan Bellmare | 1 : 0 |
| 14 | Iwata | Hokkaido Consadole Sapporo | 0 : 1 |
| 15 | Kashima Antlers | Kyoto | 2 : 1 |
| 16 | Kumamoto | Sanfrecce Hiroshima | 0 : 2 |
1/8-finals
Quarter-finals
| 1 | Yokohama F. Marinos | Oita Trinita | 2 : 1 |
| 2 | Kawasaki Frontale | Sagan Tosu | 0 : 2 |
| 3 | FC Tokyo | Vegalta Sendai | 2 : 1 |
| 4 | Kofu | Sanfrecce Hiroshima | 1 : 2 |
Semi-finals
| 1 | Yokohama F. Marinos | Sagan Tosu | 2 : 0 |
| 2 | FC Tokyo | Sanfrecce Hiroshima | 0 : 1 |
Final
| 1 | Yokohama F. Marinos | Sanfrecce Hiroshima | 2 : 0 |
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