Introduction: Adolescence is one of the life stages that play a key role and is also affected by the epidemiology transition as the result of the development of the era. Consuming a lot of fast food and junk food nowadays causes adolescents, both girls and boys, to be subjected to nutritional problems such as the high body fat percentage. Adolescent boys even tend to be unaware of their health. This study aims to analyse nutritional factors which have an effect on body fat percentage in adolescent boys. Methods: This study was performed involving 1046 high school students in 5 Jakarta districts. Spearman’s correlation and multiple linear regression were used for the data analysis of this study. Results: The result shows that there was a relationship between BMI-for-age, energy and macronutrient intakes, and body fat percentage. Adolescents with excessive intakes got affected by their body fat percentage, although their BMI-for-age is normal. The result of multivariate analysis suggests that BMI-for-age had the most effect on body fat percentage. Conclusion: There needs to be a regular education for adolescent boys to be aware of their body fat percentage and other factors that have an effect on it.