Objective: To explore the association of physical activity and screen time with health-related quality of life among students in China. Methods: A total of 4 388 students (graders 4-12) were randomly selected from primary, junior and senior high schools in Nanjing, China, to take part in this cross-sectional questionnaire survey in 2018. The associations of physical activity and screen time with health-related quality of life were assessed using mixed-effects linear regression models and reported as mean difference (MD) and 95% confidence interval(CI). Results: After adjustment for potential confounders and class-level clustering effects, students with sufficient physical activity reported an increased 0.03 (95%CI=0.01-0.05) unit of the Child Health Utility 9D (CHU9D) scores compared to their counterparts with insufficient physical activity, while participants with short screen time also recorded higher CHU9D scores 0.05(95%CI=0.02-0.08) than those with prolonged screen time. Relative to those with insufficient physical activity and prolonged screen time, students with insufficient physical activity and short screen time 0.05(95%CI=0.02-0.09), or students with sufficient physical activity and prolonged screen time 0.03(95%CI=-0.03-0.10), or students with sufficient physical activity and short screen time 0.08(95%CI=0.05-0.12), respectively, reported increased CHU9D scores. Conclusion Health-related quality of life was positively associated with physical activity, but negatively with screen time. Moreover, these two factors may have a combined effect on health-related quality of life.