| Dunes | |
| DWANGO Co., Ltd | Tokyo |
| DX Antenna Co., Ltd | Tokyo |
| Dyden Corporation | |
| DyDo Pharma, Inc. | |
| DYM Co., Ltd | Tokyo |
| DynaComware Corporation | Tokyo |
| Dynamic Pricing Technology | Osaka |
| Dynavector Systems Ltd | Tokyo |
| DYNAX Corporation | |
| Dynmon Co., Ltd | |
| e-Business Solution Co., Ltd | Tokyo |
| E-Frontier, Inc. | Tokyo |
| E-Mail.jp | Tokyo |
| E-Net | Tokyo |
| E-net Co., Ltd | Tokyo |
| e-shoppy | Hyogo |
| E-State Online Co., Ltd | Tokyo |
| e-studio Co., Ltd | Tokyo |
| e-system | Tokyo |
| E-Times Technologies Co., Ltd | Tokyo |
| EA Pharma Co., Ltd | |
| Eagle Network Co., Ltd | Fukuoka |
| Earlyworks Co., Ltd | Tokyo |
| Earth Net Co., Ltd | Tokyo |
| Earth Technology Group | Tokyo |
| Earthbrain Ltd | Tokyo |
| EASEL Co., Ltd | Kanagawa |
| East Creative, Inc. | Tokyo |
| Eastdawn | Tokyo |
| Eat Creative | |
| ECCO, Inc. | Aichi |
| Echigo BSD Users Group | Tokyo |
| Echo Electronics Industry Co., Ltd | Tokyo |
| Ecrowd, Inc. | |
| ECS Co., Ltd | Osaka |
| Eden Co., Ltd | Tokyo |
| EDGE Technology Co., Ltd | Tokyo |
| EdgeCortix, Inc. | |
| EDION Internet Service | Tokyo |
| EditForce Co., Ltd | Fukuoka |
| Edocode Co., Ltd | Tokyo |
| Edogawa University | |
| Educational Foundation and University | |
| Ef-prime, Inc. | Tokyo |
| Ehime Prefectural University of Health Sciences | |
| Ehime University | |
| Eighty Co., Ltd | Tokyo |
| Eiki Information System Co., Ltd | Tokyo |
| Eisai Co., Ltd | Tokyo |