First round

• West Kagawa High School 0–1 Kokushikan University
• YSCC 1–7 Otsuka Pharmaceuticals
• Kunimi High School 3–0 Yamagata Central High School
• Centro de Futebol Edu 3–1 Volca Kagoshima
• International Budo University 1–2 Oita Trinita
• Teihens FC 0–6 Cerezo Osaka
• Iwami FC 2–1 Fukui KSC
• Tokuyama University 0–2 Sagawa Express Osaka
• Tsukuba University 1–3 Ventforet Kofu
• Ohara Gakuen JaSRA 0–1 Avispa Fukuoka
• Fukuoka University of Education 1–2 Alouette Kumamoto
• Tochigi SC 3–1 Iwate University
• Kyushu INAX 0–5 Mito HollyHock
• Takada 0–3 Yokohama FC
• Sagawa Printing 1–0 TDK
• Denso 1–1(PK 3–1) Sapporo University
• Gunma Horikoshi 2–1 Montedio Yamagata
• Kwansei Gakuin University 2–5 Sagan Tosu
• Tokyo Gakugei University 5–1 Hachinohe University
• Saitama 2–1 YKK AP SC
• Fukushima University 1–5 Omiya Ardija
• Nangoku Kochi 1–4 Shonan Bellmare
• Sony Sendai 2–3 Japan Soccer College
• Ehime FC 6–1 Mitsubishi Nagasaki SC
• Muchz FC 0–7 Kawasaki Frontale
• Kihoku Shukyudan 0–9 Albirex Niigata
• Tottori 2–1 Alex SC
• Profesor Miyazaki 4–3 Kibi International University
• Okinawa Kariyushi 2–3 Honda FC
• Kakamihara High School 0–9 Komazawa University
• Oita Trinita U-18 1–1(PK 5–3) Sanfrecce Hiroshima Youth
• Nirasaki Astros 0–2 Hamamatsu University

Second round

• Kokushikan University 1–2 Kunimi High School
• Otsuka Pharmaceuticals 3–0 Centro de Futebol Edu
• Oita Trinita 3–0 Iwami FC
• Cerezo Osaka 4–1 Sagawa Express Osaka
• Ventforet Kofu 2–0 Alouette Kumamoto
• Avispa Fukuoka 2–1 Tochigi SC
• Mito HollyHock 4–0 Sagawa Printing
• Yokohama 3–2 Denso
• Gunma Horikoshi 0–1 Tokyo Gakugei University
• Sagan Tosu 7–0 Saitama
• Omiya Ardija 4–0 Japan Soccer College
• Shonan Bellmare 1–0 Ehime
• Kawasaki Frontale 6–0 Tottori
• Albirex Niigata 1–0 Profesor Miyazaki
• Honda 3–0 Oita Trinita U-18
• Komazawa University 1–0 Hamamatsu University

Third round

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

Fourth round

• Júbilo Iwata 2–0 Oita Trinita
• Nagoya Grampus Eight 5–2 Cerezo Osaka
• Vegalta Sendai 1–2 JEF United Ichihara
• Avispa Fukuoka 0–1 Kyoto Purple Sanga
• Kashima Antlers 1–0 Omiya Ardija
• Shimizu S-Pulse 3–2 Shonan Bellmare
• Kawasaki Frontale 1–0 Gamba Osaka
• Sanfrecce Hiroshima 2–1 Yokohama F. Marinos

Quarter finals

• Júbilo Iwata 0–1 JEF United Ichihara
• Nagoya Grampus Eight 0–1 Kyoto Purple Sanga
• Kashima Antlers 1–0 Kawasaki Frontale
• Shimizu S-Pulse 1–3 Sanfrecce Hiroshima

Semi finals

• JEF United Ichihara 0–2 Kashima Antlers
• Kyoto Purple Sanga 2–1 Sanfrecce Hiroshima

Final

• Kashima Antlers 1–2 Kyoto Purple Sanga

Kyoto Purple Sanga won the cup and guaranteed a place in the 2004 AFC Champions League But Sanga were relegated to the Division 2 in 2003 so this spot was transferred to Yokohama F. Marinos, the 2002 J.League Division 1 runner-up.