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Objectives This study aims to examine the electronic prescription programme in Iran by thoroughly identifying the key strengths, weaknesses, opportunities and threats (SWOT) associated with its implementation and utilisation among healthcare stakeholders.Design A thematic analysis was adopted, with data systematically examined through the SWOT analytical framework.Setting Hospital, pharmacy, specialised clinic, insurance affiliated clinic in Iran.Participants Participants consisted of four groups involved in implementing the electronic prescription programme, including physicians, pharmacists, nurses and hospital administrative employees. Moreover, research participants were selected using a purposive sampling approach and sampling continued until data saturation was reached.Methods Semistructured interviews were employed for data collection. The data analysis steps were systematically executed using Braun and Clarke’s six-phase thematic analysis approach. Within the study’s conceptual framework based on SWOT analysis, themes and codes were categorised into positive (strengths, opportunities) and negative (weaknesses, threats) drivers. In addition, the method proposed by Lincoln and Guba was employed to endorse the data credibility.Results Overall, data saturation was reached with 25 participants and two major themes and four minor themes. The ‘strengths’ theme comprised patient safety, economic efficiency, information sharing, remote access and drug list accessibility. The ‘weaknesses’ theme encompassed internet and electricity dependency, resistance to implementation, numerous platforms and diverse insurer schemes and frequent changes in insurance company tariffs. The ‘opportunities’ theme consisted of health system networking, clarifying processes, eliminating drug intermediaries, improving health service quality, enhancing data banks, expediting drug monitoring and improving technological infrastructures in the health field. Ultimately, the ‘threats’ theme involved confidential information access and misuse, damaged drug barcodes, incorrect data recording, patient dissatisfaction and government financial burden.Conclusions Due to the fact that the challenges and benefits associated with this system vary across countries depending on their technical and non-technical capacities and infrastructures, the findings of the current research can contribute to promoting the system within our country.