First round

• Nirasaki Astros 0–4 Hosei University
• Fukuoka University 4–1 Shimizu Commercial High School
• Gunma Fortuna 0–2 Consadole Sapporo
• Kusatsu Higashi High School 3–1 Yamagata Chuo High School
• Teihens FC 1–5 Albirex Niigata
• Ritsumeikan University 2–4 Kunimi High School
• Gifu Kogyo High School 1–7 Sagan Tosu
• Kanagawa Teachers 1–0 YKK AP SC
• Ehime FC 1–3 Yokohama FC
• Aichi Gakuin University 1–0 Fukui KSC
• Iwami FC 0–4 Shonan Bellmare
• Kochi University 1–1 (PK 4–5) Kibi International University
• Hatsushiba Hashimoto High School 0–5 Oita Trinita
• Sanfrecce Hiroshima U-18 0–1 FC Ueda Gentian
• Tenri University 0–6 Honda FC
• Nippon Steel Corporation Oita FC 4–2 Nippon Steel Kamaishi FC
• FC Primeiro 1–6 Denso SC
• Juntendo University 3–2 TDK
• SC Tottori 0–3 Omiya Ardija
• Tokuyama University 1–0 Apple Sports College
• Kwansei Gakuin University 2–1 Vegalta Sendai
• Tochigi SC 3–0 Hachinohe University
• Matsushita Electric Iga 0–4 Ventforet Kofu
• Sony Sendai 2–3 Doto University
• Saga Kita High School 0–12 Montedio Yamagata
• NIFS Kanoya 1–4 Jatco SC
• Kaiho Bank 0–3 Mito HollyHock
• Yokogawa Electric 1–1 (PK 4–5) Hannan University
• Saitama SC 0–2 Urawa Red Diamonds
• NTT Kumamoto 0–2 Honda Lock
• University of Tsukuba 4–1 Tokai University
• Sun Life FC 0–5 Otsuka Pharmaceuticals

Second round

• Hosei University 2–3 Fukuoka University
• Consadole Sapporo 6–0 Kusatsu Higashi High School
• Albirex Niigata 2–0 Kunimi High School
• Sagan Tosu 6–0 Kanagawa Teachers
• Yokohama FC 1–2 Aichi Gakuin University
• Shonan Bellmare 3–0 Kibi International University
• Oita Trinita 7–0 FC Ueda Gentian
• Honda FC 2–0 Nippon Steel Corporation Oita FC
• Denso SC 2–1 Juntendo University
• Omiya Ardija 4–1 Tokuyama University
• Kwansei Gakuin University 0–1 Tochigi SC
• Ventforet Kofu 2–1 Doto University
• Montedio Yamagata 1–2 Jatco SC
• Mito HollyHock 2–0 Hannan University
• Urawa Red Diamonds 9–0 Honda Lock
• University of Tsukuba 1–1 (PK 2–4) Otsuka Pharmaceuticals

Third round

• Yokohama F. Marinos 2–0 Fukuoka University
• Kyoto Purple Sanga 0–1 Consadole Sapporo
• Verdy Kawasaki 2–1 Albirex Niigata
• Kashima Antlers 2–1 Sagan Tosu
• Júbilo Iwata 5–0 Aichi Gakuin University
• Nagoya Grampus Eight 3–2 Shonan Bellmare
• Gamba Osaka 4–1 Oita Trinita
• Kashiwa Reysol 2–1 Honda FC
• Shimizu S-Pulse 3–0 Denso SC
• Avispa Fukuoka 4–2 Omiya Ardija
• JEF United Ichihara 1–0 Tochigi SC
• FC Tokyo 0–1 Ventforet Kofu
• Vissel Kobe 2–1 Jatco SC
• Sanfrecce Hiroshima 7–0 Mito HollyHock
• Kawasaki Frontale 0–2 Urawa Red Diamonds
• Cerezo Osaka 2–1 Otsuka Pharmaceuticals

Fourth round

• Yokohama F. Marinos 2–1 Consadole Sapporo
• Verdy Kawasaki 0–2 Kashima Antlers
• Júbilo Iwata 2–0 Nagoya Grampus Eight
• Gamba Osaka 1–1 (PK 10–9) Kashiwa Reysol
• Shimizu S-Pulse 1–0 Avispa Fukuoka
• JEF United Ichihara 3–1 Ventforet Kofu
• Vissel Kobe 1–0 Sanfrecce Hiroshima
• Urawa Red Diamonds 1–4 Cerezo Osaka

Quarter finals

• Yokohama F. Marinos 1–1 (PK 1–4) Kashima Antlers
• Júbilo Iwata 0–1 Gamba Osaka
• Shimizu S-Pulse 3–1 JEF United Ichihara
• Vissel Kobe 2–2 (PK 4–3) Cerezo Osaka

Semi finals

• Kashima Antlers 3–2 Gamba Osaka
• Shimizu S-Pulse 1–0 Vissel Kobe

Final

• Kashima Antlers 3–2 Shimizu S-Pulse

Kashima Antlers won the championship.