First round

• Brummell Sendai 7–0 Yamaga Club
• Iwami FC 0–7 Juntendo University
• Mitsubishi Nagasaki SC 2–1 Hatsushiba Hashimoto High School
• Mito HollyHock 3–0 Hokkaido Electric Power
• Nirasaki Astros 0–2 NTT Kanto
• Mitsubishi Motors Mizushima 0–0 (PK 6–7) Yamagata FC
• Kusatsu Higashi High School 0–3 Sagan Tosu
• Nara Sangyo University 3–1 Nippon Stel Corporation Oita FC
• Saga Commercial High School 1–5 Oita Trinity
• Mind House Yokkaichi 0–3 Momoyama Gakuin University
• Kansai University 0–9 Tokyo Gas
• Ehime Youth 2–1 Alo's Hokuriku
• Blaze Kumamoto 0–2 Honda
• Kwansei Gakuin University 2–6 Albirex Niigata
• Jatco 1–0 Okinawa International University
• Kagawa Shiun Club 1–0 Waseda University
• Seino Transportation 5–0 Kochi University
• Moka High School 1–5 Kokushikan University
• Tottori 0–7 Kawasaki Frontale
• Honda Luminoso Sayama 4–1 Nippon Steel Corporation Kamaishi FC
• Kanagawa University 1–3 Ventforet Kofu
• Fukuoka University 5–1 Akita City Hall
• Aoyama Gakuin University 1–0 Denso
• FC Primeiro 0–1 Hannan University
• Maebashi Shogyo High School 0–6 Fukushima FC
• Nagoya Bank 3–4 Fukui Teachers
• Kyoiku Kenkyusha 0–5 Montedio Yamagata
• Hosho High School 3–2 Takagawa Gakuen High School
• Kagoshima Shogyo High School 1–2 Consadole Sapporo
• Hiroshima University 2–3 Aster Aomori
• Otsuka Pharmaceuticals 8–1 Teihens FC
• Ichiritsu Funabashi High School 0–2 Komazawa University

Second round

• Brummell Sendai 0–1 Juntendo University
• Verdy Kawasaki 2–0 Mitsubishi Nagasaki SC
• Mito HollyHock 1–2 Avispa Fukuoka
• NTT Kanto 1–0 Yamagata FC
• Sagan Tosu 4–0 Nara Sangyo University
• Oita Trinity 1–1 (PK 3–5) Momoyama Gakuin University
• Tokyo Gas 2–1 Ehime Youth
• Honda 3–1 Albirex Niigata
• Jatco 6–0 Kagawa Shiun Club
• Seino Transportation 1–2 Kokushikan University
• Kawasaki Frontale 3–0 Honda Luminoso Sayama
• Ventforet Kofu 2–1 Fukuoka University
• Aoyama Gakuin University 0–1 Hannan University
• Fukushima 1–0 Fukui Teachers
• Montedio Yamagata 8–0 Hosho High School
• Consadole Sapporo 4–1 Aster Aomori
• Otsuka Pharmaceuticals 1–3 Komazawa University

Third round

• Kashima Antlers 4–1 Juntendo University
• Verdy Kawasaki 0–2 Avispa Fukuoka
• Urawa Red Diamonds 2–1 NTT Kanto
• Gamba Osaka 3–2 Sagan Tosu
• Yokohama Marinos 5–0 Momoyama Gakuin University
• Nagoya Grampus Eight 1–3 Tokyo Gas
• Kyoto Purple Sanga 3–2 Honda
• Bellmare Hiratsuka 7–0 Jatco
• Kashiwa Reysol 4–1 Kokushikan University
• Vissel Kobe 2–0 Kawasaki Frontale
• Cerezo Osaka 5–1 Ventforet Kofu
• Júbilo Iwata 3–0 Hannan University
• Shimizu S-Pulse 3–0 Fukushima
• Sanfrecce Hiroshima 3–1 Montedio Yamagata
• JEF United Ichihara 1–0 Consadole Sapporo
• Yokohama Flügels 4–3 Komazawa University

Fourth round

• Kashima Antlers 6–0 Avispa Fukuoka
• Urawa Red Diamonds 1–2 Gamba Osaka
• Yokohama Marinos 1–2 Tokyo Gas
• Kyoto Purple Sanga 1–5 Bellmare Hiratsuka
• Kashiwa Reysol 2–1 Vissel Kobe
• Cerezo Osaka 2–3 Júbilo Iwata
• Shimizu S-Pulse 3–1 Sanfrecce Hiroshima
• JEF United Ichihara 1–2 Yokohama Flügels

Quarterfinals

• Kashima Antlers 3–0 Gamba Osaka
• Tokyo Gas 3–2 Bellmare Hiratsuka
• Kashiwa Reysol 1–2 Júbilo Iwata
• Shimizu S-Pulse 1–6 Yokohama Flügels

Semifinals

• Kashima Antlers 3–1 Tokyo Gas
• Júbilo Iwata 2–3 Yokohama Flügels

Final

• Kashima Antlers 3–0 Yokohama Flügels

Kashima Antlers won the championship.