Background Phenylketonuria (PKU) Screening is a public health measure aimed at identifying the early cases and managing the affected infants and trying to reduce infant morbidity and mortality. The aim of this study was to analyze the policies of the PKU national screening program in Iran. Methods PKU screening program policies were analyzed according to the policy triangle model. Document review and 38 semi-structured interviews were used for data collection. Document review data were analyzed using content analysis and interview data were analyzed using framework analysis. Results The findings of the study were categorized according to the content (structure and organization, rules, bylaws and guidelines), process (agenda setting, formation, implementation, and evaluation of screening policies and programs), the policy context (political and executive factors, economic and financial factors, social and cultural factors), and the stakeholders(Genetics office, Network Development Bureau, Population and Family Health Bureau, Health Reference Laboratory, Pediatric Health Department, Health Vice-Chancellor of Medical Sciences, Health Ministry Deputy of Health, PKU Selected Hospitals, Pastor Institute, Food and Drug Administration and Research Centers. Welfare Organization, the Health Insurance Agency, the PKU Patient Support Association, the Post Company, and the Registry). Conclusions The policy triangle framework helped to explain the different components of the PKU screening program.