Background: School physical education (PE) not only offers and promotes health-related physical activity (PA), but also encompasses the promotion and development of health-related well-being such as health-related quality of life (HRQOL). Furthermore, assessing PA and HRQOL have become major issues in pediatric public health and also serve as a major goal of Healthy people 2020. Grounded in the expectancy-value and achievement goal frameworks, the primary purpose of this study was to examine the relationships among the perceptions of motivational climate in PE, expectancy-value beliefs, HRQOL, and PA among elementary children. A secondary purpose was to test whether expectancy-value beliefs mediate the relationship between motivational climate and HRQOL as well as between motivational climate and PA (self-reported PA and pedometer-based PA, respectively). Methods: Participants were 336 elementary children recruited from three public schools in the southeastern USA (M[subscript age] = 9.87; 179 girls, 157 boys). The majority of the participants (53.3%) were White students and the remainder (46.7%) including African-American (37.4%), Asian-American (1.5%), Hispanic-American (1.8%) and others (5.9%). Students completed a previously validated questionnaire assessing expectancy-related beliefs and task values toward PE. The 23-item pediatric QOL inventory generic core scale (PedsQL™ 4.0) was used to assess participants' HRQOL. Children's PA levels were assessed by using a self-reported survey (Physical Activity Questionnaire for Older Children) and three-day pedometer counts (steps/min during PE). Analysis/Results: Correlational analyses showed that expectancy-related beliefs and task values were positively related to PA and HRQOL. Regression analyses indicated that both mastery and performance motivational climate had a positive effect on children's expectancy beliefs and task values. Mediational analyses were used to evaluate the potential mediational relationships among motivational climate (independent variables: mastery and performance climates), expectancy-value beliefs (mediator: expectancy-value beliefs), and HRQOL and PA (dependent variables: total HRQOL score, self-reported PA and steps/min), respectively. Conclusions: A mastery motivational climate together with high expectancy beliefs has a positive association with HRQOL, which in turn could produce health benefits in the future. Results suggest that a performance motivational climate could be associated with less activity (i.e. lower steps/min) even when students view PE as interesting, important, and useful. One important implication of the study is that by promoting mastery climates and expectancy-value beliefs in PE practitioners can encourage children to engage in PA both in and outside of school, and consequently may influence their quality of life.