| J.League Cup | |
| Year: | 2006 |
| Other Titles: | J.League Yamazaki Nabisco Cup |
| Country: | Japan |
| Dates: | March 29 and November 3 |
| Champions: | JEF United Chiba |
| Count: | 2 |
| Runner-Up: | Kashima Antlers |
| Semi-Finalist1: | Yokohama F. Marinos |
| Semi-Finalist2: | Kawasaki Frontale |
| Player Label: | MVP Award |
| Prevseason: | 2005 |
| Nextseason: | 2007 |
The Last edition of the J.League Cup, officially the 2006 J.League Yamazaki Nabisco Cup, sponsored by Nabisco began on March 29. Gamba Osaka were exempt from competing in the group stage, due to their entry into the Asian Champions League. They were therefore entered into the quarter-final stage.
The final was on November 3 at the Tokyo National Stadium. The winners were JEF United Ichihara Chiba, beating Kashima Antlers in the final 2-0 to claim its second J.League Cup championship.
| 2006-03-29 | |||
| Urawa Red Diamonds | 2–0 | F.C. Tokyo | |
| Yokohama F. Marinos | 1–0 | Avispa Fukuoka | |
| 2006-04-12 | |||
| Urawa Red Diamonds | 3–1 | Avispa Fukuoka | |
| Yokohama F. Marinos | 2–0 | F.C. Tokyo | |
| 2006-04-26 | |||
| F.C. Tokyo | 1–2 | Yokohama F. Marinos | |
| Avispa Fukuoka | 1–3 | Urawa Red Diamonds | |
| 2006-05-14 | |||
| F.C. Tokyo | 0–1 | Avispa Fukuoka | |
| Yokohama F. Marinos | 1–2 | Urawa Red Diamonds | |
| 2006-05-17 | |||
| F.C. Tokyo | 0–0 | Urawa Red Diamonds | |
| Avispa Fukuoka | 1–1 | Yokohama F. Marinos | |
| 2006-05-21 | |||
| Urawa Red Diamonds | 4–2 | Yokohama F. Marinos | |
| Avispa Fukuoka | 0–0 | F.C. Tokyo |
| 2009-03-29 | |||
| Kashima Antlers | 4–1 | Ōita Trinita | |
| Kyoto Purple Sanga | 3–4 | Kawasaki Frontale | |
| 2009-04-12 | |||
| Kashima Antlers | 3–1 | Kawasaki Frontale | |
| Ōita Trinita | 2–1 | Kyoto Purple Sanga | |
| 2009-04-26 | |||
| Kawasaki Frontale | 4–1 | Kyoto Purple Sanga | |
| Ōita Trinita | 1–0 | Kashima Antlers | |
| 2009-05-14 | |||
| Kashima Antlers | 3–2 | Kyoto Purple Sanga | |
| Ōita Trinita | 0–2 | Kawasaki Frontale | |
| 2009-05-17 | |||
| Kawasaki Frontale | 1–0 | Ōita Trinita | |
| Kyoto Purple Sanga | 2–1 | Kashima Antlers | |
| 2009-05-21 | |||
| Kawasaki Frontale | 2–1 | Kashima Antlers | |
| Kyoto Purple Sanga | 1–2 | Ōita Trinita |
| 2006-03-29 | |||
| JEF United Chiba | 2–1 | Sanfrecce Hiroshima | |
| Albirex Niigata | 3–3 | Shimizu S-Pulse | |
| 2006-04-12 | |||
| JEF United Chiba | 3–2 | Albirex Niigata | |
| Shimizu S-Pulse | 2–2 | Sanfrecce Hiroshima | |
| 2006-04-26 | |||
| Shimizu S-Pulse | 1–2 | Albirex Niigata | |
| Sanfrecce Hiroshima | 3–4 | JEF United Chiba | |
| 2006-05-14 | |||
| Shimizu S-Pulse | 1–0 | JEF United Chiba | |
| Sanfrecce Hiroshima | 0–0 | Albirex Niigata | |
| 2006-05-17 | |||
| Sanfrecce Hiroshima | 0–1 | Shimizu S-Pulse | |
| 2006-05-18 | |||
| Albirex Niigata | 0–0 | JEF United Chiba | |
| 2006-05-21 | |||
| JEF United Chiba | 1–0 | Shimizu S-Pulse | |
| Albirex Niigata | 0–1 | Sanfrecce Hiroshima |
| 2006-03-29 | |||
| Nagoya Grampus Eight | 1–3 | Ventforet Kofu | |
| Cerezo Osaka | 1–0 | Júbilo Iwata | |
| 2006-04-05 | |||
| Júbilo Iwata | 2–1 | Omiya Ardija | |
| 2006-04-12 | |||
| Ventforet Kofu | 2–2 | Júbilo Iwata | |
| Cerezo Osaka | 1–1 | Nagoya Grampus Eight | |
| 2006-04-26 | |||
| Omiya Ardija | 2–3 | Júbilo Iwata | |
| Ventforet Kofu | 1–1 | Nagoya Grampus Eight | |
| 2006-05-10 | |||
| Ventforet Kofu | 0–1 | Cerezo Osaka | |
| Nagoya Grampus Eight | 1–2 | Omiya Ardija | |
| 2006-05-14 | |||
| Omiya Ardija | 1–0 | Ventforet Kofu | |
| Nagoya Grampus Eight | 1–1 | Cerezo Osaka | |
| 2006-05-17 | |||
| Omiya Ardija | 1–1 | Cerezo Osaka | |
| 2006-05-18 | |||
| Júbilo Iwata | 1–2 | Ventforet Kofu | |
| 2006-05-21 | |||
| Júbilo Iwata | 2–1 | Nagoya Grampus Eight | |
| Cerezo Osaka | 3–2 | Omiya Ardija |
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Kawasaki Frontale advances to the semi-finals on Away goals rule.------------
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Kashima Antlers advances to the finals on Away goals rule.----
See main article: 2006 J.League Cup Final.
Koki Mizuno (JEF United Chiba)
Washington (Urawa Red Diamonds), 9 goals Hiroyuki Taniguchi (Kawasaki Frontale)