Context: Since the onset of the COVID-19 pandemic, there have been numerous higher education challenges. Medical universities have been urged to dispel students from educational and clinical settings and led them toward virtual education. This sudden transition has been accompanied by multiple challenges. Objectives: The present study aimed to evaluate the challenges of virtual medical education in the COVID-19 pandemic. Study Selection: This systematic review was performed by reviewing the current literature on the research subject and the studies conducted in this regard during March 2019 to April 2021 by searching via five key search engines and databases, including Google Scholar, ScienceDirect, PubMed, Scopus, and ERIC. Results: In total, 23 studies were assessed, and different virtual education challenges in medical universities were classified into three categories of structural challenges, student-related challenges, and teacher-related challenges. In addition, strategies were proposed for overcoming the identified challenges. Conclusions: Since medical education was not properly pursued before the COVID-19 pandemic and the necessary infrastructures are lacking in this area, designing and implementing such programs could bring about fundamental challenges in several countries (especially developing and low-income countries), thereby decreasing their success rate. On the other hand, the coronavirus crisis could be an opportunity to identify the weaknesses, shortcomings, and infrastructural deficiencies in e-learning and address these issues effectively.