Despite the benefits of using virtual reality (VR) in medical education and treatment, some challenges and limitations result in the uselessness or misuse of this technology. Therefore, recognizing potential challenges related to VR might be helpful in the strategic decision-making process to implement and develop this technology in the healthcare field. Accordingly, our review aimed to determine the challenges associated with the application of VR in the field of medical education and treatment. We searched Science Direct, Google Scholar, and PubMed databases for relevant papers using a defined search query. We restricted the search to articles in English or Persian language published by the end of 2018. The main challenges of developing and using VR with educational and therapeutic objectives are categorized as general and specific. General challenges include reduced face-to-face communications, education, cost challenges, users' attitudes, and specific challenges such as designing, safety considerations, VR side effects, evaluation, and validation of VR applications. Challenges related to VR will have different effects, thus identifying each of them helps to determine the solutions for each challenge. Also, it is suggested to develop and update laws, standards, and protocols, which play an important role in increasing the effective application of VR at the national level.