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Abstract Background As COVID-19 has been declared as a pandemic disease by the WHO on March 11th, 2020, the global incidence of COVID-19 disease increased dramatically. In response to the COVID-19 situation, Jordan announced the emergency state on the 19th of March, followed by the curfew on 21 March. All educational institutions have been closed as well as educational activities including clinical medical education have been suspended on the 15th of March. As a result, Distance E-learning emerged as a new method of teaching to maintain the continuity of medical education during the COVID-19 pandemic related closure of educational institutions. Distance E-Learning is defined as using computer technology to deliver training, including technology-supported learning either online, offline, or both. Before this period, distance learning was not considered in Jordanian universities as a modality for education. This study aims to explore the situation of distance E-learning among medical students during their clinical years and to identify possible challenges, limitations, satisfaction as well as perspectives for this approach to learning. Methods This cross-sectional study is based on a questionnaire that was designed and delivered to medical students in their clinical years. For this study, the estimated sample size ( n = 588) is derived from the online Raosoft sample size calculator. Results A total of 652 students have completed the questionnaire, among them, 538 students (82.5%) have participated in distance learning in their medical schools amid COVID-19 pandemic. The overall satisfaction rate in medical distance learning was 26.8%, and it was significantly higher in students with previous experience in distance learning in their medical schools as well as when instructors were actively participating in learning sessions, using multimedia and devoting adequate time for their sessions. The delivery of educational material using synchronous live streaming sessions represented the major modality of teaching and Internet streaming quality and coverage was the main challenge that was reported by 69.1% of students. Conclusion With advances in technologies and social media, distance learning is a new and rapidly growing approach for undergraduate, postgraduate, and health care providers. It may represent an optimal solution to maintain learning processes in exceptional and emergency situations such as COVID-19 pandemic. Technical and infrastructural resources reported as a major challenge for implementing distance learning, so understanding technological, financial, institutional, educators, and student barriers are essential for the successful implementation of distance learning in medical education.