| Summary: | Abstract Background and Aims Primary care and the use of a referral system are essential components of any health system. The aim of this study was to investigate and identify the challenges affecting the performance of the primary health‐care system in Iran. Methods This qualitative study was carried out consisting of 14 interviews with experts and those familiar with the primary care system and its function. Purposive and snowball sampling was used to identify the samples. The recorded files were transcribed and entered into the MAXQDA‐11 software to be analyzed. The conventional content analysis approach was used for data analysis. Results The findings of this study included 72 initial codes classified into 7 main themes and 18 subthemes. Seven main themes consist of governance, manpower, resources, financial management, services delivery, trans‐sectional, and social and cultural. The greatest challenges for Iran's primary health care (PHC) system are governance and human resources problems. Conclusion Various dimensions of Iran's primary care system especially governance and human resources are facing several challenges that threaten its performance and efficiency. Policymakers and planners must address challenges fundamentally and do not get satisfied with superficial reforms that have short‐term and soothing effects. In this regard, enhancing governance functioning can profoundly solve numerous challenges of Iran's primary care system. We also suggest the strengthening of intersectoral collaboration.
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