BackgroundPhysical activity and sedentary behavior are common factors influencing cardiovascular health. However, how school and leisure-time activity/sedentary behavior are associated with physical fitness and blood lipid levels in primary school children in consideration of gender disparity remains unclear.MethodsData was obtained from a health and nutrition survey on primary school children from nine areas in China. The association between physical activities/sedentary behaviors (school and leisure-time physical activity levels, screen time, and other sedentary behaviors) and anthropometric measurements/prevalence of dyslipidemia were examined by multilevel analysis (the individual level, class level, grade level, and investigation area level) adjusted for age, energy intake and family income.ResultsA total of 770 participants (average age = 9.4 ± 1.7 years) were included. Prevalence of dyslipidemia was 10.9%. Prevalence of dyslipidemia was associated with screen time in boys [OR = 3.04, 95% CI (1.24–7.45)] and inversely associated with leisure-time physical activity in boys [OR = 2.22, 95% CI (1.08–4.56)] and school-time activity in girls [OR = 5.34, 95% CI (1.18–24.16)].ConclusionsPhysical activity—but not sedentary behavior—was significantly associated with dyslipidemia in both genders. Increasing leisure-time physical activity for boys and school-time physical activity for girls may be critical.