Background: Accordingly, the present study aimed to investigate the challenges experienced by faculty members and students in virtual education and to propose practical recommendations at Allameh Tabataba’i University.

Methods: This study employed an exploratory qualitative design using thematic analysis and was conducted as a case study at Allameh Tabataba’i University. Participants included faculty members and students who had experienced virtual education during the COVID-19 pandemic. They were selected through purposive sampling with maximum variation. Sampling continued until data saturation was achieved. Data were collected through semi-structured interviews (45–70 minutes), fully transcribed, and analyzed following the six phases of thematic analysis using the constant comparative method. Content validity of the interview guide was confirmed by nine experts (CVR = 0.89; CVI = 0.95).

Results: The identified challenges emerged at the intersection of three interrelated levels: structural (policy ambiguity, inadequate network infrastructure, privacy concerns, and copyright issues), pedagogical (continuation of lecture-based teaching, limited interactive design, and weaknesses in assessment practices), and individual–psychological (decreased motivation, cognitive fatigue, and feelings of academic isolation). Among faculty members, themes such as initial informational deficiencies, generational gaps in digital literacy, legal ambiguities regarding privacy and intellectual property, and gradual improvement in instructional quality were identified. Among students, key themes included lack of motivation, incompatibility of virtual education with active learning styles, lack of class engagement, cultural and regulatory inadequacies, weak network infrastructure, and absence of face-to-face interaction. Comparative analysis revealed that the central issue underlying these challenges was the misalignment between the nature of the virtual environment and traditional teaching practices and governance structures.

Conclusion: Improvement of virtual education requires interventions at multiple levels, including policy reform, interactive pedagogical redesign, infrastructure enhancement, and the cultivation of digital learning culture. The results may inform university policymakers in designing blended learning systems and advancing digital transformation in higher education.