Background: The spread of Coronavirus Disease 2019 (COVID-19) caused restrictions and shutdowns affecting the economic situation, employment, and the educational needs of society. Meanwhile, the universities of medical sciences have faced serious problems in education. Objectives: The present study aimed to assess the satisfaction of the students of Ghaen and Ferdows medical schools with virtual education during the COVID-19 epidemic. In addition, the factors effective in this satisfaction are investigated. Methods: This descriptive-analytical (cross-sectional) study was conducted at Ghaen School of Nursing and Midwifery and Ferdows School of Paramedical Sciences and Health, Iran, using a researcher-made questionnaire provided to students online. The study population was all the students of these two faculties. The sample size was estimated as 285 people using the Morgan table, and 296 individuals participated in the study. Data were collected and analyzed using descriptive and inferential tests by the SPSS software version 24. Results: Our findings showed that most (40.2%) students had moderate satisfaction, and only 5.74% had very high satisfaction with virtual education. The mean satisfaction of female students was higher than males without a statistically significant difference (P = 0.4). Moreover, the results of the analysis of variance revealed that the level of the academic satisfaction of students is different in distinct academic levels (P = 0.007). In addition, Pearson’s correlation coefficient indicated a significant positive correlation between age and academic satisfaction score (P = 0.001, r = 0.185). Conclusions: Overall, the results of the present study showed that less than half of the students were moderately satisfied with virtual education. According to the students, this dissatisfaction mainly results from the lack of a suitable infrastructure for virtual classes. Usually, satellite branches are weaker than the main university in terms of facilities and equipment, and solving these problems requires the special attention of education officials and managers.