1st round

• Omiya Ardija 1–0 TDK
• Mitsubishi Nagasaki SC 0–4 Chuo University
• FC Primeiro 1–0 Nihon University Yamagata High School
• Gifu Kogyo High School 1–2 Kagoshima Jitsugyo High School
• Kawasoe Club 0–6 Ventforet Kofu
• Nippon Steel Corporation Oita FC 1–3 Doto University
• Juntendo University 0–1 Otsuka Pharmaceuticals
• Sanwa Club 1–4 Tokushima Municipal High School
• Matsushita Electric Works FC 0–5 Denso
• Maebashi Ikuei High School 0–7 Tsukuba University
• Chukyo University 1–4 Tokyo Gas
• Tokai University 0–0 (PK 3–0) Teihens FC
• Kagawa Shiun Club 1–9 Kawasaki Frontale
• Niigata Shukyu-Kai 0–2 YKK AP SC
• Nirasaki Astros 2–3 Brummell Sendai
• Tokuyama University 2–4 Kansai University
• Kwansei Gakuin University 3–2 Shizuoka Sangyo University
• Teijin SC 0–6 Kokushikan University
• Iwami FC 1–9 Montedio Yamagata
• Meiji University 5–0 Nippon Steel Corporation Kamaishi FC
• Tenri University 2–3 Honda
• Hosho High School 4–1 Ueda Gentian
• Koga Club 0–9 Oita Trinita
• Kyushu Sangyo University 1–2 Ritsumeikan University
• Kyoiku Kenkyusha 0–4 Albirex Niigata
• Hannan University 3–2 Hatsushiba Hashimoto High School
• Gainare Tottori 0–3 Sagan Tosu
• Tochigi SC 3–2 Kumamoto Ohzu High School
• Fukuyama University 2–2 (PK 4–3) Fukui Teachers
• Sony Sendai 2–1 Aster Aomori
• Mito HollyHock 4–2 Mitsubishi Motors Mizushima
• Himawari Milk Nangoku SC 2–7 Komazawa University

2nd round

• Omiya Ardija 2–0 Chuo University
• Consadole Sapporo 1–0 FC Primeiro
• Kagoshima Jitsugyo High School 0–7 Vissel Kobe
• Ventforet Kofu 6–1 Doto University
• Otsuka Pharmaceuticals 4–2 Tokushima Municipal High School
• Denso 1–3 Tsukuba University
• Tokyo Gas 2–0 Tokai University
• Kawasaki Frontale 1–0 YKK AP SC
• Brummell Sendai 2–1 Kansai University
• Kwansei Gakuin University 3–1 Kokushikan University
• Montedio Yamagata 1–0 Meiji University
• Honda FC 4–0 Hosho High School
• Oita Trinita 2–1 Ritsumeikan University
• Albirex Niigata 3–1 Hannan University
• Sagan Tosu 4–0 Tochigi SC
• Kyoto Purple Sanga 9–0 Fukuyama University
• Sony Sendai 0–5 Avispa Fukuoka
• Mito HollyHock 4–3 Komazawa University

3rd round

• Júbilo Iwata 2–0 Omiya Ardija
• Consadole Sapporo 2–1 Vissel Kobe
• Cerezo Osaka 4–6 Ventforet Kofu
• Yokohama Flügels 4–2 Otsuka Pharmaceuticals
• Kashima Antlers 3–1 Tsukuba University
• Bellmare Hiratsuka 2–1 Tokyo Gas
• Sanfrecce Hiroshima 2–1 Kawasaki Frontale
• Yokohama Marinos 0–1 Brummell Sendai
• Nagoya Grampus Eight 3–1 Kwansei Gakuin University
• Gamba Osaka 1–2 Montedio Yamagata
• JEF United Ichihara 0–2 Honda FC
• Verdy Kawasaki 1–0 Oita Trinita
• Urawa Red Diamonds 4–1 Albirex Niigata
• Kashiwa Reysol 3–1 Sagan Tosu
• Kyoto Purple Sanga 2–3 Avispa Fukuoka
• Shimizu S-Pulse 5–0 Mito HollyHock

4th round

• Júbilo Iwata 3–2 Consadole Sapporo
• Ventforet Kofu 0–3 Yokohama Flügels
• Kashima Antlers 3–0 Bellmare Hiratsuka
• Sanfrecce Hiroshima 3–0 Brummell Sendai
• Nagoya Grampus Eight 3–2 Montedio Yamagata
• Honda FC 1–3 Verdy Kawasaki
• Urawa Red Diamonds 3–1 Kashiwa Reysol
• Avispa Fukuoka 2–3 Shimizu S-Pulse

Quarterfinals

• Júbilo Iwata 1–2 Yokohama Flügels
• Kashima Antlers 2–1 Sanfrecce Hiroshima
• Nagoya Grampus Eight 2–1 Verdy Kawasaki
• Urawa Red Diamonds 0–1 Shimizu S-Pulse

Semifinals

• Yokohama Flügels 1–0 Kashima Antlers
• Nagoya Grampus Eight 1–2 Shimizu S-Pulse

Final

• Yokohama Flügels 2–1 Shimizu S-Pulse

Yokohama Flügels won the championship.

This was the last match of Flügels as a club, as they merged with Yokohama Marinos. As a result, Shimizu took their place in the subsequent Xerox Super Cup and Asian Cup Winners' Cup competitions.