The purpose of this study is to describe the study design and protocol and baseline results of the “Healthy Habits, Healthy Girls” program. The intervention will be evaluated through a randomized controlled trial in 10 public schools of São Paulo. The variables were collected and evaluated at baseline and will be evaluated after 7 and 12-month baseline: body mass index, waist circumference, dietary intake, nutrition and physical activity social cognitive mediators, physical activity level, sedentary behaviors, physical self-perception, and global self-steam. The statistical analyses followed the intention-to-treat principles and mediators of nutrition and physical activity behavior change will be explored. Participated 253 adolescent girls, with 135 from the intervention group (16.32±0.78 years). The baseline results demonstrated that 32.4% and 23.4% of the intervention and control group were overweight, and for both groups more than 50% did not meet the daily recommendations for moderate and vigorous PA and for the time spent on screen activities. For most of the variables, with exception age (p=0.00) and waist circumference (p=0.01), there weren’t significant statistical differences between groups. There is a gap on the Brazilian literature about study design and protocols of school-based randomized controlled trials to prevent obesity among youth. This study might be an important contribution to the field.