Objective: To analyze trend estimates on the prevalence of risk and protective behaviors for chronic noncommunicable diseases in adolescents, according to data from the National School Health Survey in 2009, 2012 and 2015. Methods: Data from the three cross-sectional studies in Brazilian capitals and the Federal District were used. In total, 173,310 adolescents enrolled in the ninth grade of elementary school were interviewed, with average age of 14 years. The prevalence of indicators of protective (consumption of beans and fruit; physical education classes at school; practice of physical activity for 60 minutes or more) and risk factors (consumption of candies and soft drinks; use of cigarettes and alcohol in the last 30 days; drug testing) were estimated through linear regression. Results: There was a significant increase (p < 0.05) in the prevalence of fruit consumption and in the reduction of bean, soft drinks and candies consumption, as well as the consumption of alcoholic beverages and cigarettes. However, an increase in the prevalence of illicit drug experimentation was observed. Discussion: Despite the tendency to reduce risk factors, prevalences are high when compared with other sociocultural realities. Conclusion: The school is an important area of access to the adolescent public, and it is necessary to encourage school health promotion programs to reduce health risk behaviors, as well as to stimulate protective ones.