2017/06/21 | Sanfrecce Hiroshima | | 3-2 | | Kagoshima United | | | | |
| Albirex Niigata | | 2-1 Pro. | | Banditonce Kakogawa | | | | |
| Vissel Kobe | | 3-1 | | Kataller Toyama | | | | |
| Avispa Fukuoka | | 4-2 | | Miyazaki Sangyo-keiei University | | | | |
| Ehime FC | | 2-1 | | Kamatamare Sanuki | | | | |
| Shonan Bellmare | | 1-0 Pro. | | Kokushikan University | | | | |
| Zweigen Kanazawa | | 2-0 | | Yokohama FC | | | | |
| Vegalta Sendai | | 2-3 | | University of Tsukuba | | | | |
| Renofa Yamaguchi | | 1-2 | | Thespa Kusatsu | | | | |
| Sagan Tosu | | 3-0 | | Kagura Shimane | | | | |
| Matsumoto Yamaga | | 4-0 | | MD Nagasaki | | | | |
| Tokushima Vortis | | 0-3 | | Gifu | | | | |
| Nagoya Grampus | | 6-0 | | SRC Hiroshima | | | | |
| Júbilo Iwata | | 2-2 (5-4 Pen.) | | Honda FC | | | | |
| Ventforet Kofu | | 0-1 | | Vanraure Hachinohe | | | | |
| Kyoto Sanga | | 0-1 | | Azul Claro | | | | |
| Fagiano Okayama | | 0-0 (5-3 Pen.) | | Imabari | | | | |
| Omiya Ardija | | 3-0 | | Tonan Maebashi | | | | |
| Urawa Reds | | 3-2 | | Grulla Morioka | | | | |
| JEF United | | 1-0 | | Tokyo Verdy | | | | |
| Gamba Osaka | | 3-0 | | Verspah Oita | | | | |
| Kashiwa Reysol | | 1-0 | | Briobecca Urayasu | | | | |
| FC Tokyo | | 1-1 (4-5 Pen.) | | Nagano Parceiro | | | | |
| Mito Hollyhock | | 1-2 Pro. | | Roasso Kumamoto | | | | |
| Cerezo Osaka | | 2-0 | | Niigata University | | | | |
| Shimizu S-Pulse | | 4-1 | | Giravanz Kitakyushu | | | | |
| Machida Zelvia | | 2-4 | | Oita Trinita | | | | |
| Consadole Sapporo | | 2-5 Pro. | | Iwaki | | | | |
| Montedio Yamagata | | 1-0 Pro. | | V-Varen Nagasaki | | | | |
| Yokohama Marinos | | 3-1 | | FC Osaka | | | | |
| Kawasaki Frontale | | 2-0 | | Tochigi Uva | | | | |
| Kashima Antlers | | 5-0 | | Maruyasu Okazaki | | | | |