Subjective happiness is often regarded as a major life goal. Although Japan is an economically powerful country, the level of subjective well-being reported among Japanese adolescents is lower than in other countries. We aimed to investigate the lifestyle factors related to unhappiness in Japanese adolescents. We collected data through the 2017-2018 Lifestyle Survey of Adolescents, a nationally representative cross-sectional study enrolled in randomly selected junior and senior high schools throughout Japan. We assessed the prevalence of subjective unhappiness in junior and senior high school students according to school life factors and daily lifestyle habits. A multivariable logistic regression analysis was used to examine the associations between these factors and unhappiness. A total of 64,329 students were included in the sample (mean age 15.7 years, 53.9% boys). The average prevalence of unhappiness was 10.2%. The logistic regression analyses indicated that unhappiness was strongly associated with being male and with engaging in unhealthy lifestyle behaviors such as not having breakfast, poor sleep quality, and some problematic Internet usage. Although the prevalence of unhappiness was significantly higher among current smokers and alcohol drinkers, these behaviors were not associated with unhappiness in the multivariable logistic regression analysis. Unhappiness among Japanese adolescents appears to be strongly related to how they spend their daily life. We therefore consider it desirable for school officials to educate students on the importance of happiness and lifestyle factors conducive to happiness.