The controversial role of ethics in clinical education and its ability to draw the attention of a large audience is inevitable. The issues and challenges of the COVID-19 pandemic have transformed the clinical education environment. This study was conducted to explore the challenges and ethical requirements of medical sciences education during the COVID-19 pandemic in 2020. The study was qualitative research and the instrument was a semi-structured interview. The participants included faculty members of the basic and clinical Sciences at Iran University of Medical Sciences. After 16 rounds of interviews, theoretical saturation was achieved. Qualitative data were analysed using conventional content analysis, which resulted in 81 preliminary codes and 28 sub-categories. Finally, two themes of "ethical challenges" and "ethical requirements", and 10 categories were achieved. The sub-categories were consisted of "being patient-centred", "social accountability of curriculums", "ethical challenges of the clinical environment", "the poor performance of the clinical faculty members and students", "being justice-centred", "raising awareness", "observing clinical research ethics", "preservation and promotion of mental health", "patient confidentiality", and "respect for individuals". We hope the ethical challenges in medical education that were created due to the emergence of Covid-19 can be reduced and eliminated by defining a framework for ethical requirements.