Background Lifestyles are associated with physical and mental health status, as well as health-related quality of life (QOL) in adults. There is little information about relation between lifestyles and QOL in children. This study aims to examine the correlation among Japanese children. Methods Subjects were from the Toyama Birth Cohort Study, a prospective, longitudinal survey of children born between 1989 and 1990 in Toyama Prefecture, Japan. When children were 12–13 years in 2002, a cross-sectional questionnaire-based survey was administered. The questionnaire designed to measure lifestyles included questions on eating, physical activity, sleep, and other factors. For QOL measurement, a validated Japanese version of the COOP Charts was used. Data from 7,887 children were available and logistic regression analyses were used. Results Children with undesirable lifestyles, such as skipping breakfast, less participation in physical activity, longer television viewing, and later bedtime, were more likely to have poor QOL in domains of physical fitness, feelings, overall health, and quality of life. These correlations were independent of sex, BMI, social background, and somatic symptoms. Conclusions Undesirable lifestyles are positively associated with impaired QOL among children. Further understanding of these relationships will facilitate the development of interventions to help children with poor QOL.