Background and Aim: The growing health care needs of students actuated world Health Organization to develop School-based health projects in the last decades. The most important plan that has received worldwide attention and in Iran for nearly one decade is Health Promoting School (HPS) program which being implemented with collaboration of Ministries of Health and Education. Present qualitative study was conducted to evaluate this program implementation in Ahvaz education organization (District 1). Materials and Methods: In this qualitative study data was collected by semi-structured interview. The study population consisted of school health experts affiliated with Ahvaz West Health Center and health deputy, health experts affiliated with education organization (District 1 and school headmasters and expert staffs in HPS (22 persons). The sampling was purposeful and the interviews continued until saturation of data. Content analysis was used for analysis of the data. Results: Data analysis showed that most components of the HPS program in schools belong to education organization were not implemented properly. The major barriers were categorized into 5 and 47 main and subsidiary themes respectively. Poor stewardship and authority, policymaking and legislation, weaknesses in motivation, attitude and awareness of managers and experts, inadequacy in resources and infrastructure, ineptitude in program implementation and finally inappropriate evaluation system was specified as the main themes. According to results, some of the most important reasons for failure in HPS program consisted of, lack of functions definiteness between health deputy in ministry of health and education organization, job dissatisfaction in school health experts, not being a priority behalf education organization, insufficient delegation of authorized budget, lack of interpectoral cooperation between trustee organizations and indifference about program evaluation. Conclusion: The most important challenge in the HPS program is the implementation barriers that make the establishment and implementation of this program almost ineffective. The serious and committed interaction between the ministry of Health and Education and between their respective provincial and county districts can provide the foundation for the implementation of this valuable program. A review of the organizational structure and executive framework of the program is also necessary.