Objective To analyze the prevalence of metabolic syndrome (MS) in pubertal stages of female students. Methods Cross-sectional study of 449 school children between eight and 18 years, stratified by pubertal stage, body mass index (BMI) and body fat percentage (BF %). The MS was classified according to the International Diabetes Federation. The analysis by frequency distribution, confidence intervals (95 %), Chi-square and odds ratio for associations was performed. Results The prevalence of MS was 3.3 % (CI:2 %-5 %) and 2.5 % (CI: 0.1 - 5 %) in pubertal and 7.9% (CI:3.2 % - 12.6 %) in the post-pubescent, with a significant association of this group with MS (X² = 5.2 [p <0.02]). The odds ratio shows that post-pubescent girls (3.3 [CI: 1.2 to 5]) and obese girls (2.1 [CI: 2 - 2.2]) are more likely to have MS, indicating significant linear association between BMI and the outcome (X²=29.4 [p<0.001]). Pubescent children under 10 years of age with MS had higher %G. The prevalent components were altered waist circumference (27.2 % [CI23 %-31 %]) and low HDL cholesterol (39.6 % [CI 35 % - 44 %]), as well as prevalence of systemic hypertension in post-pubertal girls. Conclusions MS begins in the pubertal stage, with prevalence in the post-pubertal stage. Excess fat is a trigger in children under 10 years of age. Prevention strategies are needed for the population of children and adolescents.