First round

• Hiroshima University of Economics 4–0 Sanyo Electric Tokushima
• Gainare Tottori 3–2 TDK
• Mitsubishi Motors Mizushima 3–2 Renaiss Gakuen Kōga
• Alouette Kumamoto 5–2 Mitsubishi Heavy Industries Nagasaki
• Oita Trinita U-18 1–0 Fuji University
• Hachinohe University 3–1 Central Kobe
• Saga University 2–0 Haguro High School
• FC Ryukyu 3–0 Yamaguchi Teachers
• Kochi University 2–1 Hannan University
• Honda Lock 4–1 Teikyo Daisan High School
• Sony Sendai 6–1 Maruoka High School
• Japan Soccer College 1–0 Chukyo High School

Second round

• Sony Sendai 5–0 Yumoto High School
• Sagawa Printing 2–1 Mitsubishi Motors Mizushima
• Momoyama Gakuin University 2–0 National Institute of Fitness and Sports in Kanoya
• Tochigi SC 1–0 Gainare Tottori
• FC Ryukyu 1–0 Fukuoka University
• Tenri University 3–1 Saga University
• Ehime FC 3–0 Kochi University
• Tokai University 3–2 Otsuka Pharmaceuticals
• Sagawa Express Tokyo SC 2–0 Ryutsu Keizai University
• Honda FC 3–2 Sapporo University
• Gunma Horikoshi 2–1 Luminoso Sayama
• Hachinohe University 8–3 Yokkaichi University
• Thespa Kusatsu 6–0 Mattō FC
• Oita Trinita U-18 2–1 Kihoku Shūkyūdan
• Honda Lock 4–1 Nagano Elsa
• ALO's Hokuriku 2–0 Hiroshima University of Economics
• Japan Soccer College 0–0 (PK 4–2) JEF United Ichihara Amateur
• Chukyo University 2–1 Komazawa University
• Alouette Kumamoto 2–0 Takamatsu Kita High School
• FC Central Chūgoku 1–1 (PK 5–4) Shizuoka FC

Third round

• Thespa Kusatsu 1–0 Momoyama Gakuin University
• Shonan Bellmare 1–0 Hachinohe University
• Ventforet Kofu 1–0 Sony Sendai FC
• Omiya Ardija 2–1 ALO's Hokuriku
• Gunma Horikoshi 2–1 Tokai University
• Yokohama FC 4–0 Oita Trinita U-18
• Avispa Fukuoka 9–1 Tenri University
• Montedio Yamagata 3–2 FC Ryukyu
• Sagan Tosu 2–0 Tochigi SC
• Consadole Sapporo 2–1 Honda Lock
• Vegalta Sendai 2–0 Sagawa Printing
• Kyoto Purple Sanga 11–2 Japan Soccer College
• Kawasaki Frontale 4–0 Ehime FC
• Mito HollyHock 4–0 Alouette Kumamoto
• Honda FC 8–0 FC Central Chūgoku
• Sagawa Express Tokyo SC 3–2 Chukyo University

Fourth round

• Yokohama F. Marinos 2–1 Montedio Yamagata
• Gamba Osaka 3–1 Sagan Tosu
• Gunma Horikoshi 1–0 Kashiwa Reysol
• Omiya Ardija 1–0 Shimizu S-Pulse
• Júbilo Iwata 3–2 Sagawa Express Tokyo SC
• FC Tokyo 1–0 Vegalta Sendai
• Kashima Antlers 1–0 Mito HollyHock
• Tokyo Verdy 2–1 Kyoto Purple Sanga
• Shonan Bellmare 3–2 Albirex Niigata
• Avispa Fukuoka 1–3 Urawa Red Diamonds
• Thespa Kusatsu 2–1 Cerezo Osaka
• Consadole Sapporo 2–1 JEF United Ichihara
• Kawasaki Frontale 3–2 Vissel Kobe
• Yokohama FC 1–0 Sanfrecce Hiroshima
• Oita Trinita 2–1 Ventforet Kofu
• Nagoya Grampus Eight 3–0 Honda FC

Fifth round

• Júbilo Iwata 2–1 Gunma Horikoshi
• Tokyo Verdy 2–1 Nagoya Grampus Eight
• Kashima Antlers 3–2 Kawasaki Frontale
• Consadole Sapporo 1–0 Oita Trinita
• Gamba Osaka 5–0 Yokohama FC
• FC Tokyo 6–3 Omiya Ardija
• Yokohama F. Marinos 1–2 Thespa Kusatsu
• Urawa Red Diamonds 3–0 Shonan Bellmare

Quarterfinals

• Thespa Kusatsu 0–3 Tokyo Verdy
• Kashima Antlers 0–1 Gamba Osaka
• Urawa Red Diamonds 2–1 FC Tokyo
• Consadole Sapporo 0–1 Júbilo Iwata

Semi finals

Final

• Tokyo Verdy 2–1 Júbilo Iwata

Tokyo Verdy won the championship.