| 24 May 25 | r01    | Mito HollyHockMito HollyHoc | 0 - 1 | SagamiharaSagamihara |
| 24 May 25 | r01 | Nara ClubNara Club | 3 - 1 | Niigata University H and Niigata Unive |
| 24 May 25 | r01 | FC GifuFC Gifu | 3 - 1 | Toyama ShinjoToyama Shinjo |
| 24 May 25 | r01 | Tochigi SCTochigi SC | 5 - 0 | Oyama SCOyama SC |
| 24 May 25 | r01 | Sendai UniversitySendai Univer | 2 - 4 | Toyo UniversityToyo Universi |
| 24 May 25 | r01 | Kyoto Sangyo UniversityKyoto Sangyo | 3 - 1 | Moriyama Samurai 2000Moriyama Samu |
| 24 May 25 | r01 | Brew SagaBrew Saga | 2 - 1 | Hirondelle KumamotoHirondelle Ku |
| 24 May 25 | r01 | Veroskronos TsunoVeroskronos T | 2 - 1 | Gainare TottoriGainare Totto |
| |
| 24 May 25 | r00 | Ehime FCEhime FC | 1 - 0 | Mitsubishi NagasakiMitsubishi Na |
| |
| 24 May 25 | r01 | Kamatamare SanukiKamatamare Sa | 1 - 1 | Kochi UnitedKochi United |
| 25 May 25 | r01 | Matsumoto YamagaMatsumoto Yam | 2 - 1 | FC OsakaFC Osaka |
| 25 May 25 | r01 | Okinawa SVOkinawa SV | 4 - 1 | Verspah OitaVerspah Oita |
| 25 May 25 | r01 | ImabariImabari | 0 - 2 | Kagoshima UnitedKagoshima Uni |
| 25 May 25 | r01 | Zweigen KanazawaZweigen Kanaz | 6 - 0 | Chukyo UniversityChukyo Univer |
| 25 May 25 | r01 | Arterivo WakayamaArterivo Waka | 4 - 3 | Basara HyogoBasara Hyogo |
| 25 May 25 | r01 | Thespa GunmaThespa Gunma | 1 - 0 | Hosei UniversityHosei Univers |
| 25 May 25 | r01 | ReinMeer AomoriReinMeer Aomo | 5 - 0 | BTOP HokkaidoBTOP Hokkaido |
| 25 May 25 | r01 | Fukui UnitedFukui United | 1 - 0 | Honda FCHonda FC |
| 25 May 25 | r01 | Veertien MieVeertien Mie | 1 - 0 | Yamanashi Gakuin UniversiYamanashi Gak |
| 25 May 25 | r01 | Fukushima UnitedFukushima Uni | 9 - 1 | Tokyo International UniveTokyo Interna |
| 25 May 25 | r01 | Iwate Grulla MoriokaIwate Grulla | 6 - 0 | North Asia UniversityNorth Asia Un |
| 25 May 25 | r01 | Belugarosso IwamiBelugarosso I | 0 - 1 | Giravanz KitakyushuGiravanz Kita |
| 25 May 25 | r01 | Kataller ToyamaKataller Toya | 2 - 1 | Juntendo UniversityJuntendo Univ |
| 25 May 25 | r01 | Fukuyama CityFukuyama City | 2 - 1 | FC TokushimaFC Tokushima |
| 25 May 25 | r01 | Oita TrinitaOita Trinita | 2 - 0 | Lvnirosso NCLvnirosso NC |
| 25 May 25 | r01 | Baleine ShimonosekiBaleine Shimo | 2 - 1 | International Pacific UniInternational |
| 25 May 25 | r01 | RB Omiya ArdijaRB Omiya Ardi | 0 - 1 | University of TsukubaUniversity of |
| |
| 11 Jun 25 | r02 | Tokushima VortisTokushima Vor | 2 - 1 | Renofa YamaguchiRenofa Yamagu |
| 11 Jun 25 | r02 | Yokohama F MarinosYokohama F Ma | 0 - 2 | ReinMeer AomoriReinMeer Aomo |
| 11 Jun 25 | r02 | Machida ZelviaMachida Zelvi | 2 - 1 | Kyoto Sangyo UniversityKyoto Sangyo |
| 11 Jun 25 | r02 | Nagoya GrampusNagoya Grampu | 3 - 0 | Veroskronos TsunoVeroskronos T |
| 11 Jun 25 | r02 | Sanfrecce HiroshimaSanfrecce Hir | 3 - 1 | Brew SagaBrew Saga |
| 11 Jun 25 | r02 | JEF United ChibaJEF United Ch | 1 - 1 | Roasso KumamotoRoasso Kumamo |
| 11 Jun 25 | r02 | Vegalta SendaiVegalta Senda | 0 - 1 | Kataller ToyamaKataller Toya |
| 11 Jun 25 | r02 | Shimizu S-PulseShimizu S-Pul | 4 - 2 | Matsumoto YamagaMatsumoto Yam |
| 11 Jun 25 | r02 | Fagiano OkayamaFagiano Okaya | 0 - 2 | Giravanz KitakyushuGiravanz Kita |
| 11 Jun 25 | r02 | Avispa FukuokaAvispa Fukuok | 2 - 0 | Okinawa SVOkinawa SV |
| 11 Jun 25 | r02 | Kashima AntlersKashima Antle | 4 - 0 | Thespa GunmaThespa Gunma |
| 11 Jun 25 | r02 | Montedio YamagataMontedio Yama | 2 - 1 | Kagoshima UnitedKagoshima Uni |
| 11 Jun 25 | r02 | Kawasaki FrontaleKawasaki Fron | 4 - 3 | Fukushima UnitedFukushima Uni |
| 11 Jun 25 | r02 | IwakiIwaki | 1 - 2 | Blaublitz AkitaBlaublitz Aki |
| 11 Jun 25 | r02 | Sagan TosuSagan Tosu | 1 - 0 | Ehime FCEhime FC |
| 11 Jun 25 | r02 | Tokyo VerdyTokyo Verdy | 3 - 1 | Tochigi SCTochigi SC |
| 11 Jun 25 | r02 | Kyoto SangaKyoto Sanga | 1 - 0 | Nara ClubNara Club |
| 11 Jun 25 | r02 | Shonan BellmareShonan Bellma | 2 - 0 | FC GifuFC Gifu |
| 11 Jun 25 | r02 | Júbilo IwataJúbilo Iwata | 1 - 2 | SagamiharaSagamihara |
| 11 Jun 25 | r02 | Vissel KobeVissel Kobe | 4 - 1 | Kochi UnitedKochi United |
| 11 Jun 25 | r02 | Cerezo OsakaCerezo Osaka | 5 - 0 | Arterivo WakayamaArterivo Waka |
| 11 Jun 25 | r02 | Fujieda MYFCFujieda MYFC | 2 - 0 | Baleine ShimonosekiBaleine Shimo |
| 11 Jun 25 | r02 | V-Varen NagasakiV-Varen Nagas | 2 - 1 | University of TsukubaUniversity of |
| 11 Jun 25 | r02 | Albirex NiigataAlbirex Niiga | 1 - 0 | Fukuyama CityFukuyama City |
| 11 Jun 25 | r02 | Ventforet KofuVentforet Kof | 2 - 1 | Fukui UnitedFukui United |
| 11 Jun 25 | r02 | Kashiwa ReysolKashiwa Reyso | 0 - 2 | Toyo UniversityToyo Universi |
| 18 Jun 25 | r02 | Yokohama FCYokohama FC | 2 - 1 | Iwate Grulla MoriokaIwate Grulla |
| 18 Jun 25 | r02 | Gamba OsakaGamba Osaka | 2 - 1 | Veertien MieVeertien Mie |
| 18 Jun 25 | r02 | FC TokyoFC Tokyo | 3 - 1 | Zweigen KanazawaZweigen Kanaz |
| 18 Jun 25 | r02 | Hokkaido Consadole SapporHokkaido Cons | 2 - 2 | Oita TrinitaOita Trinita |
| |
| 16 Jul 25 | r03 | Cerezo OsakaCerezo Osaka | 2 - 0 | Tokushima VortisTokushima Vor |
| 16 Jul 25 | r03 | ReinMeer AomoriReinMeer Aomo | 1 - 2 | Blaublitz AkitaBlaublitz Aki |
| 16 Jul 25 | r03 | Kawasaki FrontaleKawasaki Fron | 0 - 0 | SagamiharaSagamihara |
| 16 Jul 25 | r03 | Vissel KobeVissel Kobe | 2 - 1 | Ventforet KofuVentforet Kof |
| 16 Jul 25 | r03 | Nagoya GrampusNagoya Grampu | 2 - 1 | Roasso KumamotoRoasso Kumamo |
| 16 Jul 25 | r03 | Albirex NiigataAlbirex Niiga | 1 - 2 | Toyo UniversityToyo Universi |
| 16 Jul 25 | r03 | Tokyo VerdyTokyo Verdy | 1 - 0 | Sagan TosuSagan Tosu |
| 16 Jul 25 | r03 | Gamba OsakaGamba Osaka | 4 - 4 | Montedio YamagataMontedio Yama |
| 16 Jul 25 | r03 | FC TokyoFC Tokyo | 2 - 0 | Oita TrinitaOita Trinita |
| 16 Jul 25 | r03 | Machida ZelviaMachida Zelvi | 2 - 1 | Kataller ToyamaKataller Toya |
| 16 Jul 25 | r03 | Kashima AntlersKashima Antle | 2 - 1 | V-Varen NagasakiV-Varen Nagas |
| 16 Jul 25 | r03 | Avispa FukuokaAvispa Fukuok | 0 - 0 | Giravanz KitakyushuGiravanz Kita |
| 16 Jul 25 | r03 | Shonan BellmareShonan Bellma | 0 - 1 | Shimizu S-PulseShimizu S-Pul |
| 16 Jul 25 | r03 | Sanfrecce HiroshimaSanfrecce Hir | 5 - 2 | Fujieda MYFCFujieda MYFC |
| 16 Jul 25 | r03 | Kyoto SangaKyoto Sanga | 3 - 3 | Yokohama FCYokohama FC |
| |
| 06 Aug 25 | r04 | FC TokyoFC Tokyo | 2 - 1 | Cerezo OsakaCerezo Osaka |
| 06 Aug 25 | r04 | Sanfrecce HiroshimaSanfrecce Hir | 3 - 0 | Shimizu S-PulseShimizu S-Pul |
| 06 Aug 25 | r04 | Machida ZelviaMachida Zelvi | 1 - 0 | Kyoto SangaKyoto Sanga |
| 06 Aug 25 | r04 | Vissel KobeVissel Kobe | 2 - 1 | Toyo UniversityToyo Universi |
| 06 Aug 25 | r04 | Kashima AntlersKashima Antle | 3 - 2 | Avispa FukuokaAvispa Fukuok |
| 06 Aug 25 | r04 | SagamiharaSagamihara | 2 - 1 | Blaublitz AkitaBlaublitz Aki |
| 06 Aug 25 | r04 | Montedio YamagataMontedio Yama | 1 - 2 | Urawa Red DiamondsUrawa Red Dia |
| 13 Aug 25 | r04 | Tokyo VerdyTokyo Verdy | 1 - 2 | Nagoya GrampusNagoya Grampu |
| |
| 27 Aug 25 | QF | Machida ZelviaMachida Zelvi | 3 - 0 | Kashima AntlersKashima Antle |
| 27 Aug 25 | QF | Nagoya GrampusNagoya Grampu | 2 - 4 | Sanfrecce HiroshimaSanfrecce Hir |
| 27 Aug 25 | QF | SagamiharaSagamihara | 1 - 1 | Vissel KobeVissel Kobe |
| 27 Aug 25 | QF | FC TokyoFC Tokyo | 2 - 1 | Urawa Red DiamondsUrawa Red Dia |
| |
| 16 Nov 25 | SF | Machida ZelviaMachida Zelvi | 2 - 0 | FC TokyoFC Tokyo |
| 16 Nov 25 | SF | Vissel KobeVissel Kobe | 2 - 0 | Sanfrecce HiroshimaSanfrecce Hir |
| |
| 22 Nov 25 | Final | Machida ZelviaMachida Zelvi | 3 - 1 | Vissel KobeVissel Kobe |
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