Background Online education has gained popularity in various fields, including medicine, owing to its flexibility and time-saving advantages. The COVID-19 pandemic has further accelerated its adoption as an alternative to traditional in-person learning. Medical students appreciate the ability to study at their own pace, access resources remotely, and engage in virtual collaboration and networking. Objective The objective of this study was to determine the perception of online education among medical students. Method A cross-sectional descriptive study was conducted at Kathmandu University School of Medical Sciences (KUSMS), Nepal, comprising 332 participants. A Google Form questionnaire was used to assess their perceptions and responses deliberated on a three-point Likert scale. Descriptive analysis was used to determine the respondents' views. Result The results showed that a significant majority (64.8%) of the respondents agreed that accessing the internet for online education was easy. However, only 35.5% felt comfortable attending online lectures at home. Regarding the effectiveness of online learning, the majority (66.3%) disagreed that it was similar to traditional classroom lectures. More than half (51.5%) of the respondents agreed that online classes were time-consuming and (71%) required breaks during sessions. Surprisingly, only 27% expressed a preference for online education. Additionally, a notable proportion (87%) disagreed that online education could provide similar real-world skills. Moreover, the majority (85%) disagreed that conducting exams for theoretical and practical/clinical courses virtually was possible. Conclusion Despite the availability of internet access for the majority of students, a significant proportion expressed discomfort with online education. Only a quarter preferred it, and many disagreed that it could replicate the traditional classroom experience or provide comparable skills. Training all faculties, providing high-speed internet, improving student interaction, and giving online demonstrations can enhance student preferences and online quality.