Electronic cigarette (e-cigarette) use has become increasingly widespread throughout the world, including in Japan. However, little is known about how e-cigarettes are used in Japan, a country with heavy restrictions on nicotine-containing e-liquids and/or vaping products. This study examined e-cigarette use (e-cigarette use duration, frequency of use, device type, electrical resistance, nicotine use, favorite e-liquid flavors) among users in Japan, through an online survey using a web-based self-reported questionnaire which included questions about sex, age, combustible cigarette and heated tobacco product (HTP) use behaviors. Of 4689 e-cigarettes users analyzed, 93.5% were men and 52.9% had been using e-cigarettes for 1–3 years. Over 80% used e-cigarettes every day; 62.3% used nicotine liquid, and half of the nicotine liquid users used nicotine salt. The most popular liquid flavor was fruit (prevalence: 68.1%), followed by tobacco (prevalence: 48.4%). While 50.9% were e-cigarette single users, 35.2% were dual users (e-cigarettes and cigarettes or HTPs) and 13.8% were triple user (e-cigarettes, cigarettes and HTPs). This is the first comprehensive survey of Japanese e-cigarette users and our finding suggest more than half use nicotine liquid, although e-cigarettes containing nicotine liquid have been prohibited by the Pharmaceutical Affairs Act since 2010 in Japan. The study also showed 49.1% of participants used cigarettes and/or HTPs concurrently (dual or triple users).