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Electronic prescribing systems have been implemented for years in developed countries, whereas developing countries have limited experience in this field. In Iran, electronic prescribing officially replaced paper-based prescriptions in January 2022. Despite its numerous advantages, the system has imposed multiple challenges on patients, pharmacies, and other stakeholders. This study aimed to explore these challenges from the perspectives of patients and community pharmacists in Mashhad, Iran. This qualitative phenomenological study was conducted with 22 participants, including patients and pharmacists working in community pharmacies in Mashhad. Data were collected through face-to-face semi-structured interviews and analyzed using qualitative content analysis. Coding and categorization were performed using MAXQDA Analytics Pro 2020. A total of 496 codes were extracted and categorized into four overarching themes: (1) challenges of the electronic prescribing system, (2) proposed solutions, (3) SWOT analysis (strengths, weaknesses, opportunities, and threats), and (4) future outlook. The main challenges were divided into pharmacy-related and patient-related challenges. The most frequently reported subthemes were “reduced workflow speed” among pharmacists and “internet and infrastructure problems” among patients. Stakeholders reported diverse challenges related to the electronic prescribing system. Internet disruptions and prescription confirmation failures, which result in delays or non-dispensing of medications, along with insufficient physician cooperation in registering and correcting prescriptions, have contributed to dissatisfaction among pharmacists and patients. Lack of integration among insurance servers, process complexity, and limited access to patients’ medication histories have further compounded these issues. Strengthening technical infrastructure and implementing comprehensive training programs for patients, pharmacists, and physicians are essential to improving system performance and stakeholder satisfaction.

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