BACKGROUND: The prevalence of childhood hypertension (HT) is growing exponentially, influenced by environmental factors such as foods with high salt content, sedentary lifestyles, and poor-quality food. The incidence of HT is about 10.4% in well-nourished children, but when associated with obesity or overweight, this can rise to 38% and 68%, respectively. To assess the influence of physical activity on the blood pressure (BP) of children who are overweight or obese. METHODS: This randomized clinical trial was carried out in Granada (Spain), from October 2015 to June 2016. The sample consisted of 98 children, all of whom were overweight or obese. The intervention group (IG) (n = 49) practised physical activity and received nutritional advice, while the control group (n = 49) only received theoretical-practical sessions on nutrition. Body composition was measured, a nutritional assessment was made and BP was determined (in percentiles, to avoid the misclassification of children who are located at the extremes of normal growth). RESULTS: Before the physical activity intervention, 85.7% of the children in the IG (with overweight/obesity) were in the 95th or higher percentile for BP, a situation representative of high BP (HT). However, by the end of the study period, this value had decreased significantly (P = 0.001), to 16.13%. CONCLUSIONS: Childhood obesity is a risk factor for HT. Physical activity, together with nutritional advice, effectively reduces BP in children who are overweight or obese. The use of percentiles, according to age, weight, and height, is an effective means of measuring BP. CLINICAL TRIALS REGISTRATION: This study is registered at https://www.clinicaltrials.gov (identifier NCT02779647).