Background In Lebanon, childhood obesity doubled during the past decade. Preventive measures should start early in life and Schools are considered an important environment to promote energy balance health behaviours. School-based programmes promoting healthy lifestyles are lacking. The purpose of this study was to evaluate the feasibility and effectiveness of a multicomponent school-based intervention to promote healthy eating and physical activity (and prevent obesity) with school children aged 9–11 years in Lebanon. Methods The intervention was developed based on the constructs of the Social Cognitive Theory and adapted to the culture of Lebanese and Arab populations. It consisted of three components: class curriculum, family involvement and food service. Eight schools were purposively selected from two communities of different socioeconomic status (SES) in Beirut and, within each school type, were matched on SES, religious sect profile, and then randomly assigned to either the intervention or control group. Anthropometric measurements and questionnaires on determinants of behavioural change, eating and physical activity habits were completed by the students in both groups at baseline and post intervention. Focus group interviews were conducted in intervention schools at the end of the study. Challenges encountered during the programme implementation were also identified, since Lebanon is considered a country with political unrest and no similar research projects were conducted in the area. Results Students in the intervention group reported purchasing and consuming less chips and sweetened drinks post-intervention compared with controls (86% & 88% less respectively p < 0.001). Knowledge and self-efficacy scores increased for the intervention (+2.8 & +1.7 points respectively p < 0.001) but not for the control group. There was no difference in physical activity and screen time habits and no changes in BMI between groups at post intervention. Interview data from focus groups showed that the programme was generally well accepted. Limitations for better outcomes include the length of the programme and the school environment. Conclusion “Health-E-PALS” intervention is a promising innovative, theory-based, culturally sensitive intervention to promote healthy eating habits and physical activity in Lebanese school children with a potential to be scaled up, replicated and sustained.