2024
1/64-finals
| 1 | YSCC | Mito | 1 : 0 |
| 2 | Bye | FC Tokyo | |
| 3 | Fukushima Utd | Kumamoto | 1 : 2 |
| 4 | Bye | Sagan Tosu | |
| 5 | Nara Club | Bye | |
| 6 | Bye | Sanfrecce Hiroshima | |
| 7 | Kagoshima Utd | Chiba | 1 : 0 |
| 8 | Bye | Verdy | |
| 9 | Yamaga | Renofa Yamaguchi | 4 : 3 |
| 10 | Bye | Avispa Fukuoka | |
| 11 | Kusatsu | Sagamihara | 4 : 1 |
| 12 | Bye | Kashiwa Reysol | |
| 13 | Gifu | Omiya Ardija | 1 : 2 |
| 14 | Bye | Nagoya Grampus | |
| 15 | Tegevajaro Miyazaki | Okayama | 1 : 4 |
| 16 | Bye | Yokohama FC | |
| 17 | Azul Claro Numazu | Vegalta Sendai | 3 : 2 |
| 18 | Bye | Hokkaido Consadole Sapporo | |
| 19 | Nagano | Tokushima | 5 : 1 |
| 20 | Bye | Kyoto | |
| 21 | Imabari | Bye | |
| 22 | Bye | Vissel Kobe | |
| 23 | Toyama | Montedio Yamagata | 2 : 1 |
| 24 | Bye | Shimizu S-Pulse | |
| 32 | Bye | Yokohama F. Marinos | |
| 33 | Kofu | Bye | |
| 48 | Bye | Kawasaki Frontale | |
| 49 | Grulla Morioka | Tochigi SC | 1 : 0 |
| 50 | Bye | Cerezo Osaka | |
| 51 | Ryukyu | Fujieda MYFC | 2 : 1 |
| 52 | Bye | Gamba Osaka | |
| 53 | Vanraure | Kanazawa | 1 : 0 |
| 54 | Bye | Kashima Antlers | |
| 55 | Giravanz Kitakyushu | Oita Trinita | 1 : 0 |
| 56 | Bye | Machida | |
| 57 | Osaka | Iwaki | 0 : 2 |
| 58 | Bye | Albirex Niigata | |
| 59 | Kamatamare | Blaublitz | 0 : 2 |
| 60 | Bye | Shonan Bellmare | |
| 61 | Gainare Tottori | Bye | |
| 62 | Bye | Urawa Reds | |
| 63 | Ehime | V-Varen Nagasaki | 3 : 4 |
| 64 | Bye | Iwata |
1/32-finals
| 1 | YSCC | FC Tokyo | 0 : 4 |
| 2 | Kumamoto | Sagan Tosu | 0 : 1 |
| 3 | Nara Club | Sanfrecce Hiroshima | 0 : 6 |
| 4 | Kagoshima Utd | Verdy | 0 : 1 |
| 5 | Yamaga | Avispa Fukuoka | 1 : 2 |
| 6 | Kusatsu | Kashiwa Reysol | 1 : 3 |
| 7 | Omiya Ardija | Nagoya Grampus | 0 : 2 |
| 8 | Okayama | Yokohama FC | 3 : 4 |
| 9 | Azul Claro Numazu | Hokkaido Consadole Sapporo | 1 : 3 |
| 10 | Nagano | Kyoto | 3 : 2 |
| 11 | Imabari | Vissel Kobe | 1 : 2 |
| 12 | Toyama | Shimizu S-Pulse | 1 : 0 |
| 16 | Bye | Yokohama F. Marinos | |
| 17 | Kofu | Bye | |
| 24 | Bye | Kawasaki Frontale | |
| 25 | Grulla Morioka | Cerezo Osaka | 0 : 1 |
| 26 | Ryukyu | Gamba Osaka | 2 : 1 |
| 27 | Vanraure | Kashima Antlers | 1 : 2 |
| 28 | Giravanz Kitakyushu | Machida | 1 : 2 |
| 29 | Iwaki | Albirex Niigata | 0 : 2 |
| 30 | Blaublitz | Shonan Bellmare | 2 : 1 |
| 31 | Gainare Tottori | Urawa Reds | 2 : 5 |
| 32 | V-Varen Nagasaki | Iwata | 1 : 0 |
1/16-finals
| 1 | FC Tokyo | Sagan Tosu | 2 : 1 |
| 2 | Sanfrecce Hiroshima | Verdy | 3 : 2 |
| 3 | Avispa Fukuoka | Kashiwa Reysol | 1 : 2 |
| 4 | Nagoya Grampus | Yokohama FC | 3 : 1 |
| 5 | Hokkaido Consadole Sapporo | Nagano | 2 : 1 |
| 6 | Vissel Kobe | Toyama | 1 : 2 |
| 8 | Bye | Yokohama F. Marinos | |
| 9 | Kofu | Bye | |
| 12 | Bye | Kawasaki Frontale | |
| 13 | Cerezo Osaka | Ryukyu | 1 : 0 |
| 14 | Kashima Antlers | Machida | 0 : 2 |
| 15 | Albirex Niigata | Blaublitz | 2 : 0 |
| 16 | Urawa Reds | V-Varen Nagasaki | 0 : 1 |
1/8-finals
| 1 | FC Tokyo | Sanfrecce Hiroshima | 1 : 3, 1 : 2 |
| 2 | Kashiwa Reysol | Nagoya Grampus | 0 : 1, 1 : 1 |
| 3 | Hokkaido Consadole Sapporo | Toyama | 2 : 1, 1 : 1 |
| 4 | Bye | Yokohama F. Marinos | |
| 5 | Kofu | Bye | |
| 6 | Bye | Kawasaki Frontale | |
| 7 | Cerezo Osaka | Machida | 2 : 2, 1 : 3 |
| 8 | Albirex Niigata | V-Varen Nagasaki | 1 : 1, 2 : 1 |
Quarter-finals
| 1 | Sanfrecce Hiroshima | Nagoya Grampus | 1 : 3, 1 : 0 |
| 2 | Hokkaido Consadole Sapporo | Yokohama F. Marinos | 3 : 1, 1 : 6 |
| 3 | Kofu | Kawasaki Frontale | 1 : 1, 0 : 1 |
| 4 | Machida | Albirex Niigata | 2 : 0, 0 : 5 |
Semi-finals
| 1 | Nagoya Grampus | Yokohama F. Marinos | 1 : 2, 3 : 1 |
| 2 | Kawasaki Frontale | Albirex Niigata | 0 : 2, 1 : 4 |
Final
| 1 | Nagoya Grampus | Albirex Niigata | 4 : 3 |
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