Rare diseases (RDs) affect up to 8% of the world's population, and unfortunately, health professionals have a low level of knowledge regarding the impacts of RDs on the social, psychological, and economic spheres of the patients and their families; hence, RD management is inadequate, consistently empirical, and precarious. The objective of this study was to determine the knowledge level of the medical students from a non-state university and physicians from Lima, Peru of RDs through a virtual survey for an analytical cross-sectional study. A total of 338 medical students and 382 physicians were surveyed. Results showed that several of the respondents (68.1% of students and 48.7% of physicians) had heard of the term "rare disease", but only a few stated that they had received any kind of training specific to it. Of the physicians, 46.6% considered that there should be a course about RDs in medical curricula, and more than 60% considered RDs a public health problem. Most respondents prioritized the planning of a higher budget for common diseases and believe it is convenient to allocate a specific fund for RDs. More than half of the participants had a very poor knowledge level. Due to students and physicians' low level of general knowledge of RDs, it is important to raise awareness and improve their education about these pathologies because this will have beneficial effects for RD patient care.