Background In undergraduate medical education virtual patients (VPs) are a suitable method to teach clinical reasoning and support the visualization of this thinking process in a safe environment. The aim of our study was to investigate differences in the clinical reasoning process and diagnostic accuracy of female and male medical students. Methods During the summer term 2020, we provided access to 15 VPs for undergraduate students enrolled in a medical school in Bavaria, Germany. All interactions of the 179 learners within the VP system CASUS were recorded, exported, and analyzed. Results We found significant differences in the clinical reasoning of female and male learners. Female students documented more findings, differential diagnoses, tests, and treatment options and more often created a summary statement about the VP. Their overall performance was higher than those of their male peers, but we did not see any significant differences in diagnostic accuracy. Conclusions The significant differences between male and female medical students should be considered when planning teaching and research activities. A future study should investigate whether these differences can also be found in physicians.