The 2006 edition of the J. League 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.
Kawasaki Frontale advances to the semi finals on Away goals rule.
Kashima Antlers advances to the finals on Away goals rule.