Background: Human lifestyles, including sedentary activities, obesity, and smoking, are associated with a high risk of non-communicable diseases that are a leading cause of death globally. Accordingly, health promotion should be done as early as possible in the adolescent period. Aims: This study explores the efficacy of a peer-educator program in promoting the healthy habits of adolescents, via an existing Indonesian community initiative program called ‘POSBINDU’ (Integrated Counseling Post), led by the general practitioners. Methods: Twenty-week ‘experiential learning’ approach with mixed-method was designed to: 1) Train 10 GP trainers, 2) Recruit and observe the 10 group-1 and 50 group-2 peer-educators in a high school; 3) Develop modules on health lifestyles by the GPS and peer-educators, and 4) Implement the POSBINDU program at the high school. Results: Both GPs and students’ perceptions significantly increased before to after the intervention ( p > 0.05). The participants also expressed they experienced increased comprehension of NCDs and the importance of healthy habits. Conclusions: The existing POSBINDU community's initiative program can potentially be improved by appropriate interventions to empower school students towards better healthy habits to prevent the early progression of NCDs.