1st Round

• Denso 3–1 Juntendo University
• Blaze Kumamoto 2–1 Kwansei Gakuin University
• World Blitz Koyama 0–7 Vissel Kobe
• Nippon Bunri University 1–3 Mitsubishi Motors Mizushima
• Kaiho Bank SC 0–4 Montedio Yamagata
• Renaiss Gakuen Koga SC 1–1 (PK 5–3) Hokkaido University
• Morioka Zebra 0–5 Fujitsu
• Fukuoka University 2–2 (PK 5–4) Albireo Niigata
• Kawasoe Club 2–5 Ventforet Kofu
• FC Matsue 0–9 Kokushikan University
• Matsuyama University 0–11 Brummell Sendai
• Tokai University 1–0 Osaka University of Commerce
• Wakayama University 0–3 Consadole Sapporo
• Gonohe City Hall 2–1 Sanyo FC
• Fukushima 2–1 Hitachi Shimizu SC
• Teihens FC 0–4 Tsukuba University
• NTT Kanto 2–0 Doshisha University
• YKK AP SC 0–5 Waseda University
• Mind House Yokkaichi 1–5 Tokyo Gas
• FC Ueda Gentian 1–2 Kunimi High School
• Central Chugoku 0–3 Tosu Futures
• Sony Sendai 2–1 Hiroshima Teachers
• Tenri University 0–1 Cosmo Oil Yokkaichi FC
• Prima Ham Tsuchiura 2–3 Komazawa University
• Tokushima Shogyo High School 1–5 Oita Trinity
• Volca Kagoshima 3–1 TDK
• Yamagata FC 1–7 Otsuka Pharmaceutical
• Kochi University 8–1 Miyazaki Teachers
• Aoyama Gakuin University 0–4 Honda
• Toa University 3–4 Kagawa Shiun Club
• Maruoka High School 0–4 Seino Transportation SC
• Yonago Higashi High School 0–4 Kansai University

2nd Round

• Denso 3–1 Blaze Kumamoto
• Vissel Kobe 4–2 Mitsubishi Motors Mizushima
• Montedio Yamagata 6–0 Renaiss Gakuen Koga SC
• Fujitsu 3–0 Fukuoka University
• Ventforet Kofu 1–2 Kokushikan University
• Brummell Sendai 4–1 Tokai University
• Consadole Sapporo 4–0 Gonohe City Hall
• Fukushima 3–0 Tsukuba University
• NTT Kanto 1–0 Waseda University
• Tokyo Gas 8–0 Kunimi High School
• Tosu Futures 5–2 Sony Sendai
• Cosmo Oil Yokkaichi FC 3–0 Komazawa University
• Oita Trinity 6–1 Volca Kagoshima
• Otsuka Pharmaceutical 2–1 Kochi University
• Honda 3–2 Kagawa Shiun Club
• Seino Transportation SC 1–2 Kansai University

3rd Round

• Yokohama Flügels 4–0 Denso
• Kyoto Purple Sanga 4–3 Vissel Kobe
• Gamba Osaka 4–1 Montedio Yamagata
• JEF United Ichihara 0–0 (PK 4–5) Fujitsu
• Kashiwa Reysol 1–0 Kokushikan University
• Sanfrecce Hiroshima 2–0 Brummell Sendai
• Shimizu S-Pulse 1–0 Consadole Sapporo
• Júbilo Iwata 1–2 Fukushima
• Urawa Red Diamonds 3–0 NTT Kanto
• Cerezo Osaka 3–1 Tokyo Gas
• Bellmare Hiratsuka 1–0 Tosu Futures
• Nagoya Grampus Eight 0–1 Cosmo Oil Yokkaichi FC
• Verdy Kawasaki 4–0 Oita Trinity
• Yokohama Marinos 1–2 Otsuka Pharmaceutical
• Avispa Fukuoka 3–1 Honda
• Kashima Antlers 2–0 Kansai University

4th Round

• Yokohama Flügels 0–1 Kyoto Purple Sanga
• Gamba Osaka 3–1 Fujitsu
• Kashiwa Reysol 1–2 Sanfrecce Hiroshima
• Shimizu S-Pulse 2–1 Fukushima
• Urawa Red Diamonds 4–0 Cerezo Osaka
• Bellmare Hiratsuka 3–1 Cosmo Oil Yokkaichi FC
• Verdy Kawasaki 4–0 Otsuka Pharmaceutical
• Avispa Fukuoka 0–2 Kashima Antlers

Quarterfinals

• Kyoto Purple Sanga 2–3 Gamba Osaka
• Sanfrecce Hiroshima 3–0 Shimizu S-Pulse
• Urawa Red Diamonds 3–0 Bellmare Hiratsuka
• Verdy Kawasaki 2–1 Kashima Antlers

Semifinals

• Gamba Osaka 0–2 Sanfrecce Hiroshima
• Urawa Red Diamonds 0–3 Verdy Kawasaki

Final

• Sanfrecce Hiroshima 0–3 Verdy Kawasaki

Verdy Kawasaki won the championship.