Background: The majority of obese children live in developing countries. The ten-fold increase in obesity during the last four decades necessitates implementing interventions to mitigate the long-term effect of obesity into adulthood. The study aimed to determine the impact of physical activity and nutrition intervention on the body mass index (BMI), blood pressure and selected biochemical factors of overweight and obese children aged 13.0 to 16.1 years from eThekweni, South Africa. Methods: Participants (N = 41) with a BMI >85th percentile were included in the 10- week controlled trial of physical activity and nutrition education intervention. Baseline and end measurements included BMI, blood pressure, and fasting biochemical variables (glucose, cholesterol, insulin resistance and alanine aminotransferase). BMI was classified according to the WHO BMI z-scores. The 10- week intervention entailed combined aerobic and resistance exercises supervised twice a week together with once-a-week nutrition intervention. Participants performed additional unsupervised aerobic exercises three times a week. Results: Elevated systolic blood pressure (52%), low-density lipoprotein levels (29%), insulin (17%) and insulin resistance values (15%) were identified. The 10-week intervention programme significantly decreased BMI (30.8 ± 5.4 kg/m2 to 29.8 ± 5.7 kg/m2; p < 0.01), systolic blood pressure (125.9 ± 15.7 mmHg to 115.2 ± 12.4 mmHg; p < 0.05), and low density lipoprotein cholesterol (2.63 mmol/L to 2.37 mmol/L; p < 0.05). Controlling for pre-testing variables as covariates, additional ANCOVA analysis highlighted significantly lower BMI (M = 28.33, F = 7.88, p < 0.05) and BMI z-scores (M = 2.08, F = 4.99, p < 0.05) in the intervention group post-testing. Conclusion: A 10-week physical activity and nutrition education intervention in overweight and obese adolescents significantly reduced BMI and showed trends of a decrease in blood pressure and low-density lipoprotein cholesterol.