This study reviewed the effectiveness of school-based physical activity interventions aimed at reducing overweight, obesity and hypertension in children. We searched 14 databases and analyzed studies published between April 2009 and September 2012. Only randomized controlled trials performed at the school level that included elements of physical activity but did not include nutritional co-interventions were analyzed. Studies were assessed by two recommended tools (EPHPP and GRADE), and the standardized mean differences with 95% confidence intervals were collected for a random-effect meta-analysis. A total of 12 papers were included in the meta-analysis, and these were divided according to three outcomes: body mass index (11 trials, n = 4,273, -0.02, 95% CI: -0.13 to 0.17, p = 0.8); body weight (5 trials, n = 1,330, -0.07, 95% CI: -0.18 to 0.04, p = 0.2); and blood pressure (6 trials, n = 1,549), including systolic (0.11, 95% CI: -0.10 to 0.31, p = 0.3) and diastolic pressure (-0.00, 95% CI: -0.10 to 0.10, p = 0.9). This meta-analysis of data from 11 randomized, school-based physical activity interventions suggests that, regardless of the potential benefits of physical activity in the school environment, the interventions did not have a statistically significant effect. However, it is difficult to generalize from these results because the duration, intensity and type of physical activity used in the interventions varied greatly.