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Introduction: Identifying the strengths and weaknesses of evaluation and quality assurance of an e-learning system can help design the systematic structure of the evaluation process in the higher education to elevate the quality of education. In view of this, this study endeavored to elaborate on the strengths and weaknesses of evaluation and quality assurance of e-learning in medical universities. Methods: This qualitative study was conducted by conventional (inductive) content analysis method in the academic year 2020 in Ahvaz University of Medical Sciences. The population consisted of professors, director of the EDC, educational vice-chancellor/president of university. The sample size was selected using purposive sampling. Semi-structured electronic questionnaire was used to collect data and Granheim and Landman content analysis approach was used to analyze the data. Results: The analysis of qualitative data obtained from 153 questionnaires from 46 universities of medical sciences was done in two main areas: strength and weakness including 17 main categories and 65 sub-categories. Strength includes providing e-learning evaluation tools, Stakeholders monitoring and feedback, assessment and adaptation of virtual lesson plans with curriculum, using the system for evaluation, developing protocols and evaluation mechanisms, forming an accreditation committee, so on. Weakness includes lack of comprehensive evaluation and quality assurance protocol, lack of evaluation infrastructure in Navid system, quantification and attention to the number of contents, ambiguity in ensuring the safety of final exams, so on. Conclusion: Providing standards and developing an evaluation mechanism can increase the quality of the e-learning evaluation process and make it easier to implement.