Statistics of Emperor's Cup in the 1999 season.

It was contested by 80 teams, and Nagoya Grampus Eight won the championship.

• Juntendo University 2–0 Aichi Gakuin University
• Tochigi SC 0–2 Júbilo Iwata Youth
• Kusatsu Higashi High School 0–2 Tokyo
• Hatsushiba Hashimoto High School 2–1 Hachinohe University
• Nippon Bunri University 1–2 Sagan Tosu
• Nagoya SC 3–4 Jatco SC
• Maebashi Shogyo High School 1–2 Ventforet Kofu
• Sony Sendai 2–1 Iwate University
• Maruoka High School 1–11 Otsuka Pharmaceuticals
• Yamaguchi Teachers 2–3 Fukuoka University
• Blaze Kumamoto 0–8 Montedio Yamagata
• Okinawa International University 0–2 Teihens FC
• FC Primeiro 0–2 Albirex Niigata
• National Institute of Fitness and Sports in Kanoya 1–0 Konan University
• Nara Sangyo University 2–7 Denso
• Iwami FC 7–3 Tokushima Shogyo High School
• Kunimi High School 0–4 Kokushikan University
• Senshu University 1–0 Yamagata FC
• Hiroshima University 0–6 Oita Trinita
• Kakamihara High School 2–8 ALO's Hokuriku
• Hannan University 1–2 Consadole Sapporo
• Mind House Yokkaichi 2–1 Mitsubishi Motors Mizushima
• Nankoku Kochi FC 3–7 Honda
• Kagawa Shiun Club 4–3 Nissei Industries FC
• Honda Lock 0–5 Vegalta Sendai
• Mito HollyHock 5–1 TDK
• Ibaraki Sakai High School 0–6 Omiya Ardija
• Nirasaki Astros 4–4 (PK 2–4) Doto University
• Ehime FC 0–3 Kawasaki Frontale
• Josai University 4–1 Kyushu INAX
• Ritsumeikan University 2–1 Tsukuba University
• Yokohama FC 8–0 Niigata University

• Juntendo University 3–0 Júbilo Iwata Youth
• FC Tokyo 6–0 Hatsushiba Hashimoto High School
• Sagan Tosu 2–1 Jatco SC
• Ventforet Kofu 0–0 (PK 3–4) Sony Sendai
• Otsuka Pharmaceuticals 0–2 Fukuoka University
• Montedio Yamagata 3–0 Teihens FC
• Albirex Niigata 1–0 NIFS Kanoya
• Denso 7–0 Iwami FC
• Kokushikan University 1–2 Senshu University
• Oita Trinita 10–0 ALO's Hokuriku
• Consadole Sapporo 3–0 Mind House Yokkaichi
• Honda FC 6–0 Kagawa Shiun Club
• Vegalta Sendai 1–2 Mito HollyHock
• Omiya Ardija 3–0 Doto University
• Kawasaki Frontale 5–1 Josai University
• Ritsumeikan University 1–4 Yokohama FC

• Bellmare Hiratsuka 3–4 FC Tokyo (aet)
• Kashima Antlers 1–0 Sagan Tosu
• Nagoya Grampus Eight 4–0 Sony Sendai
• Cerezo Osaka 4–1 Fukuoka University
• Vissel Kobe 0–0 Montedio Yamagata (aet, 3-4 pen)
• Urawa Red Diamonds 3–1 Albirex Niigata
• Kashiwa Reysol 4–2 Denso
• Kyoto Purple Sanga 1–0 Oita Trinita
• Avispa Fukuoka 1–0 Consadole Sapporo
• Sanfrecce Hiroshima 3–2 Honda FC
• Yokohama F. Marinos 2–1 Mito HollyHock
• Gamba Osaka 1–0 Omiya Ardija
• JEF United Ichihara 2–3 Kawasaki Frontale
• Verdy Kawasaki 3–2 Yokohama FC (aet)
• Jubilo Iwata 2–0 Juntendo University
• Shimizu S-Pulse 2–1 Senshu University

• Júbilo Iwata 3–0 Tokyo
• Kashima Antlers 1–2 Nagoya Grampus Eight
• Cerezo Osaka 3–4 Montedio Yamagata
• Urawa Red Diamonds 0–2 Kashiwa Reysol
• Shimizu S-Pulse 2–2 (PK 4–2) Kyoto Purple Sanga
• Avispa Fukuoka 1–2 Sanfrecce Hiroshima
• Yokohama F. Marinos 2–1 Gamba Osaka
• Kawasaki Frontale 1–3 Verdy Kawasaki

• Júbilo Iwata 0–1 Nagoya Grampus Eight
• Montedio Yamagata 0–2 Kashiwa Reysol
• Shimizu S-Pulse 0–2 Sanfrecce Hiroshima
• Yokohama F. Marinos 0–1 Verdy Kawasaki

• Nagoya Grampus Eight 2–0 Kashiwa Reysol
• Sanfrecce Hiroshima 7–2 Verdy Kawasaki

• Nagoya Grampus Eight 2–0 Sanfrecce Hiroshima

Nagoya Grampus Eight won the championship.

• (in Japanese) NHK