Background <p>For the complete implementation of an electronic prescription system, it is inevitable to consider the stakeholders’ viewpoints of the system. Given that every system should be evaluated, this study was conducted aimed to explain the experiences of stakeholders in designing evaluation criteria for the electronic prescribing system in Iran: a qualitative study.</p> Methods <p>This study is a qualitative study using directed content analysis. Interviews were conducted with 36 stakeholders of the Electronic prescription system (13 physicians, 11 pharmacists, 7 managers and experts of insurance organizations, and 5 patients) who were selected by purposive sampling. For data analysis, the criteria of Graneheim and Lundman (2004) were used, and MAXQDA 10 was used to manage the data.</p> Results <p>From the viewpoint of the participants, the criteria considered for evaluating the Electronic prescription system were “infrastructure”, “transparency and accountability”, “access to patient data”, “reminder, renewals, and monitoring”, “selection of drug and para-clinical services”, “viewing patient records”, “warning prescribers and users to support the decision”, “security and confidentiality” and “data transfer and storage”.</p> Conclusions <p>The study results can help the policymakers, managers, and decision-makers in the field of Electronic prescription systems to compare different electronic prescribing systems, the result will lead to the improvement and improvement of the electronic prescribing system in Iran.</p>