Background and purpose: Health education in Iran faces numerous challenges and obstacles that affect its quality and effectiveness. Identifying and addressing these obstacles could improve the current situation. Therefore, the present study was conducted to explore the obstacles and challenges of health education within the comprehensive health system of Birjand, Iran.  Materials and methods: This study employed a qualitative design with a conventional content analysis approach. Twelve personnel from the health care system of Birjand were selected to explore their perspectives on the obstacles and challenges of health education in fall 2023. Semi-structured, face-to-face interviews were conducted until data saturation was reached, with an average duration of 30 minutes per interview. Data were analyzed using the deductive content analysis framework of Elo and Kyngäs.  Results: A total of 136 initial codes were extracted from the interviews. After merging, these codes were organized into 26 codes, 17 sub-classes, 6 sub-categories, and 2 main categories. The sub-categories included: weaknesses in policy-making and management, factors related to employees, factors related to clients, weaknesses in inter-organizational cooperation, weaknesses in programs, and weaknesses in infrastructure. The two main categories were human barriers and non-human barriers.  Conclusion: The study results highlight significant human and non-human barriers in health education. Given the multidimensional nature of these barriers, it is essential to develop a comprehensive and coordinated program at multiple policymaking levels to address the challenges in health education, with the active participation of stakeholders, including managers, experts, and community members. Furthermore, the impact of such a program on society should be evaluated continuously across different levels of the health system.