Background: The measures taken to contain the COVID-19 pandemic, led to significant changes in university education, resulting in the new normal standard of virtual teaching in many undergraduate medical schools worldwide. Therefore, the aim of this paper was to determine the factors related to academic satisfaction with virtual teaching in medical students during the COVID-19 pandemic. Methods: A cross-sectional-analytical study was conducted on medical students at a private university in Peru, through self-reported questionnaires divided into sociodemographic data and variables of interest that could influence academic satisfaction during the pandemic. To evaluate possible factors related to academic satisfaction, stepwise regression models were performed for both sexes. Results: In total, data from 310 medical students, 117 males and 193 females, were analyzed. Academic satisfaction reached a score of 11.2 ± 2.9, which was similar in both sexes. The best regression model for males (AIC: 544.32; RMSE: 2.42; R2: 0.30) showed that adaptation to university life (favorable change) and depression (unfavorable change) explained 30% of changes in students' academic satisfaction. While in females (AIC: 907.59; RMSE: 2.49; R 2: 0.22) the model integrated favorable factors such as adjustment to college life and anxiety; while depression and poor sleep quality were unfavorable factors. Conclusion: Factors that contributed to academic satisfaction in medical students were determined in this study, which differed by gender. Thus, it is important to take into account the particularities of male and female medical students in order to improve their academic satisfaction during their university careers.