Background: The Health Promoting School Initiative (HPSI) was launched by the World Health Organization (WHO) in 1995 based on the concept of an interrelationship between education and health. In 2010, WHO supported the Lebanese Ministry of Education and Higher Education (MEHE) and established a network of 10 Health Promoting Schools (HPS). This study was undertaken to address the extent to which the HPS model was able to enhance the health of adolescents and prepare them to respond to evolving health challenges. Method: A cross-sectional survey was carried out during the academic year 2011–2012 and involved a comparison between the 10 HPS networks and 10 other public and private schools, with a total of 2,105 students (Grades 6–9). The Youth Risk Behavior Survey (CDC, 2011) and anthropometric measurements were used for data collection. Results: Findings revealed that the current school health program (SHP) failed to address issues of concern to adolescents, with prevalence of risk behaviors related to dietary and exercise practices. Neither the HPS nor control schools had a strong impact on students’ health behaviors. Conclusion: Revision of the health education curriculum is strongly needed to integrate issues concerning healthy nutrition and physical activity. Expected learning outcomes need be designed to match students’ age, grade level, and developmental milestones. The HPS network needs reassessment for project outcomes.