Aim: In the 21st century, despite advanced technology, pandemics and natural disasters have forced universities to evacuate their classrooms. As a result, there has been a shift from conventional to online education. This study aimed to examine the advantages and disadvantages of online education for preclinical medical students. Methods: This cross-sectional study was conducted between November 2020 and May 2021. The study population comprised preclinical medical students of the Marmara University–Eastern Mediterranean University (EMU) Joint Medical Program. The survey form used in the study was prepared using Google Forms, and a special link was sent to all students via the Microsoft Teams platform used for distance education. The survey included four sections, namely, demographic characteristics, advantages of online education, disadvantages of online education, and references of students. Results: The survey was sent to all students (n = 155) enrolled in the preclinical program, and 112 students (72%) participated in the study. Of the participants, 63.4% were women; moreover, 38.4% were Turkish, 31.3% were Turkish Cypriot, and 30.3% were international students. The number of students in the first, second, and third years were 35, 51, and 26, respectively. The most common advantages of online education were a chance to review missed parts of the lesson (97.3%), an opportunity to plan the study time (59.8%), and increased comfort (54.5%). The majority of the students indicated that they faced numerous challenges during online education. The most common issues were the difficulty in learning practical lessons, lack of socializing, ineffective communication, technical issues during online classes, less interactive lectures that resulted in concentration loss, and difficulty in obtaining answers from lecturers. Of the surveyed students, 48.2% preferred conventional education, only 9.8% favored online education, and 42% preferred hybrid education. Conclusions: Preclinical students at Marmara University–EMU Joint Medical Program prefer conventional education over online education. Although rewatching a lecture is a key advantage of online education, it is associated with several disadvantages for medical students. However, distance education seems to have become inevitable owing to factors such as diseases, natural disasters, and wars in the region as well as advancements in information technology. Therefore, it is necessary to conduct further research to overcome the limitations.