| Yokohama National University | |
| Yokohama National University - Kosaka Laboratory | |
| Yokohama Soei University | |
| Yokohama University of Art and Design | |
| Yokohama University of Pharmacy | |
| 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 |
| YOSIO Electronic Co., Ltd | |
| 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 |
| Yusen Logistics Co., Ltd | Tokyo |
| Yutaka Electric Manufacturing Co., Ltd | Tokyo |
| Yuto Hands Co., Ltd | Tokyo |
| YUWA Corporation | |
| YZ Co., Ltd | Tokyo |
| Z Corporation Co., Ltd | Tokyo |
| Z Venture Capital Corporation | Tokyo |
| Zaikei - IT-Science | Tokyo |
| Zanden Audio Systems | Osaka |
| Zappa Co., Ltd | Tokyo |
| ZAQ | Tokyo |
| ZeGraph | Osaka |
| Zeku Corporation | Tokyo |
| Zelas Co., Ltd | Tokyo |
| Zen Intelligence, Inc. | |
| Zen-Cart | Tokyo |
| ZENET Co., Ltd | Tokyo |
| Zenis Co., Ltd | Tokyo |
| Zephyr Systems Co., Ltd | Tokyo |
| ZERIA Pharmaceutical Co., Ltd | |
| Zero Internet Provider | Tokyo |
| Zero-Ten Co., Ltd | Fukuoka |
| Zeroboard, Inc. | |
| ZeroCAD | Osaka |
| Zerosoft Co., Ltd | Tokyo |
| Zest Co., Ltd | Tokyo |