Background Understanding human anatomy is fundamental to building medical competencies. This study explored the diverse perceptions of medical students in Saudi Arabia and Egypt concerning virtual dissection applications. Methods Students from different Saudi and Egyptian governmental universities were invited. The online questionnaire covered the sociodemographic characteristics, students’ perception of the advantages of virtual anatomy applications, satisfaction with their efficiency, and their recommendation to use them. Comparisons were performed in country-wise and then university-wise patterns. Significance was considered with a P < 0.05. Results The mean age of 401 participants was 20 ± 1.6. Females were 63% and the males were 37%. Saudi universities participated by 47% and Egyptian universities by 53% with various academic levels. The traditional program covers 25% of the participants and 75% are in integrated programs. Virtual dissection applications were used by 84% of the sample while the remaining 16% did not use them. No significant differences between Saudi participants and those from Egypt in the adopted teaching methods and the usual use of virtual dissection applications. However, significant differences in considering the ease of virtual applications (P = 0.016), their perfectness in lectures (P = 0.04), and their perception (P = 0.034). Also, there was no significant difference in satisfaction while their recommendation differed significantly (P = 0.034). The university-wise comparisons elaborated significant differences in the feasibility, reality, usefulness, preference, and perfectness of virtual dissection applications in lecturing. Conclusion Technology can be an efficient complementary, not a replacement resource to support the educational process. Also, students’ perceptions are valuable in maximizing the educational benefits of curricula.