The study determined the relationship between physical activity (PA) and risk factors of obesity among primary school children (boys: mean age 11.17±1.29, n=678; girls: mean age 10.88±1.27, n=683) in Limpopo and Mpumalanga provinces, South Africa. The children were classified according to age and sex-specific body mass index (BMI) categories (underweight: 0<18, normal weight: 18.5<25, overweight: 25<30 or obese: >30) and their blood pressure (BP) measurements. Health-related fitness was assessed with standardised test protocols. Using the International PA Questionnaire (IPAQ), the children’s PA levels were judged as: Low (METs scores of less than 500); Moderate (METs scores from 500 to 1499) or High (METs >1500). The children were mostly underweight (74%) compared to other weight categories (normal weight: 23.7%; overweight: 1.0%; obese: 0.6%). Girls had non-significant elevated BP values (systolic: 112.94±11.28mmHg; diastolic: 79.40±12.80mmHg) than boys (systolic: 110.71±14.95mmHg; diastolic: 75.53±12.53mmHg) who had higher PA levels (METs = 1286.72±317.47) than girls (METs = 397.28±30.14) (p<0.01). The children’s PA level correlated positively with BMI (.86) (p<0.01) but negatively with %BF (-.67); weight circumference (WC) (-.41); SUP (sit-up) (-.22); and predicted VO2max (-.17) (p<0.05). BMI positively associated with SBP (standing broad jump) (.06) and SAR (sit-and-reach) (.16) (p<01) whereas, it was negatively related with DBP (-.15); %BF (- .67); WC (-.26); SUP (-.21) and predicted VO2max (-.12) (p<0.05). Understanding the relationship between body composition, PA and non-communicable disease risk among children could provide a reliable basis for designing appropriate intervention programmes needed to optimise health outcomes.