Statistics of Empress's Cup in the 2006 season.

It was contested by 32 teams, and Tasaki Perule FC won the championship.^[1]

• Nagoya FC 0-3 Kibi International University
• FC Adooma 0-4 Waseda University
• Libelta Tokushima FC 0-6 Kagoshima Kamoike FC Asahina
• Kamimura Gakuen High School 3-1 Kanagawa University
• FC Re've 0-14 Hinomoto Gakuen High School
• Osaka University of Health and Sport Sciences 2-1 Seiwa Gakuen High School
• Fujieda Junshin High School 1-0 Fukui University of Technology Fukui High School
• Nippon TV Menina 3-2 Tokiwagi Gakuken High School

• Renaissance Kumamoto FC 0-2 Kibi International University
• Waseda University 1-0 Albirex Niigata
• JEF United Chiba 6-0 Kagoshima Kamoike FC Asahina
• Kamimura Gakuen High School 0-2 AS Elfen Sayama FC
• Bunnys Kyoto SC 3-2 Hinomoto Gakuen High School
• Osaka University of Health and Sport Sciences 1-4 Fukuoka J. Anclas
• Ohara Gakuen JaSRA 5-0 Fujieda Junshin High School
• Nippon TV Menina 2-0 Shimizudaihachi SC

• Nippon TV Beleza 9-0 Kibi International University
• Waseda University 0-2 TEPCO Mareeze
• INAC Leonessa 4-1 JEF United Chiba
• AS Elfen Sayama FC 1-2 Okayama Yunogo Belle
• Tasaki Perule FC 6-1 Bunnys Kyoto SC
• Fukuoka J. Anclas 2-3 Iga FC Kunoichi
• Speranza FC Takatsuki 0-2 Ohara Gakuen JaSRA
• Nippon TV Menina 0-4 Urawa Reds

• Nippon TV Beleza 4-0 TEPCO Mareeze
• INAC Leonessa 1-1 (pen 3-5) Okayama Yunogo Belle
• Tasaki Perule FC 2-0 Iga FC Kunoichi
• Ohara Gakuen JaSRA 0-4 Urawa Reds

• Nippon TV Beleza 0-1 Okayama Yunogo Belle
• Tasaki Perule FC 2-2 (pen 4-3) Urawa Reds

• Okayama Yunogo Belle 0-2 Tasaki Perule FC

Tasaki Perule FC won the championship.