In Japan, which has an aging society with many deaths, it is important that people discuss preferred place for end-of-life care in advance. This study aims to investigate whether the preferred place of end-of-life care differs by the assumed clinical scenario. This clinical scenario-based survey used data from a nationwide survey conducted in Japan in December 2017. Participants aged 20 years and older were randomly selected from the general population. The survey contained questions based on three scenarios: cancer, end-stage heart disease, and dementia. For each scenario, respondents were asked to choose the preferred place of end-of-life care among three options: home, nursing home, and medical facility. Eight hundred eighty-nine individuals participated in this study (effective response rate: 14.8%). The proportions of respondents choosing home, nursing home, and medical facility for the cancer scenario were 49.6%, 10.9%, and 39.5%, respectively; for the end-stage heart disease scenario, 30.5%, 18.9%, and 50.6%; and for the dementia scenario, 15.2%, 54.5%, and 30.3% (p < 0.0001, chi-square test). The preferred place of end-of-life care differed by the assumed clinical scenario. In clinical practice, concrete information about diseases and their status should be provided during discussions about preferred place for end-of-life care to reveal people's preferences more accurately.