| Yamaguchi Gakugai University | |
| Yamaguchi Prefectural University | |
| Yamaguchi University | Yamaguchi |
| Yamaichi Electronics Co., Ltd | Tokyo |
| Yamanashi Eiwa College | |
| Yamanashi Gakuin University | |
| Yamanashi Internet, Inc. | Tokyo |
| Yamanashi Prefectural University | |
| Yamane Medical Co., Ltd | Tokyo |
| Yamaquchi Junior College | |
| Yamato University | |
| Yappli Co., Ltd | Tokyo |
| Yashima Gakuen | |
| Yashimasokki Co., Ltd | Saitama |
| Yaskawa Electric Corporation | Fukuoka |
| Yasuda Women's University | |
| Yayoi Co., Ltd | Tokyo |
| YDC Corporation | Tokyo |
| YES Corporation | Tokyo |
| Yes We Can Co., Ltd | Tokyo |
| YL Biologics Co., Ltd | Tokyo |
| Yodogawa Hu-Tech Co., Ltd | Osaka |
| Yokkaichi Nursing and Medical Care University | |
| Yokkaichi University | |
| Yokogawa Electric Corporation | |
| Yokohama City University | |
| Yokohama College of Commerce | |
| Yokohama Densi Seiko Co., Ltd | Kanagawa |
| Yokohama National University | |
| Yokohama National University - Kosaka Laboratory | |
| Yokohama Soei University | |
| Yokohama University of Art and Design | |
| Yokosuka Research Park, Inc. | |
| Yokosuka Telecom Research Park, Inc. | Kanagawa |
| Yokota Associates Co., Ltd | Tokyo |
| Yokowo Co., Ltd | Tokyo |
| Yokozuna Data | Tokyo |
| Yonago Shinko Co., Ltd | Tokyo |
| Yoshinogawa Electric Wire & Cable Co., Ltd | Tokyo |
| You Communications Corporation | Kanagawa |
| Youworks Co., Ltd | Tokyo |
| YS Solutions Co., Ltd | Tokyo |
| Yuasa System Co., Ltd | Okayama |
| Yudo Co., Ltd | Tokyo |
| Yukioka School of Allied Health Professions | |
| Yukisoft | Tokyo |
| Yumekobo Co., Ltd | Hyogo |
| Yumeni Co., Ltd | Tokyo |
| Yumex Co., Ltd | Tokyo |
| Yupiteru Corporation | Tokyo |