Aim: Since the emergence and spread of the COVID-19, the use of E-learning has accelerated throughout the world, so education does not stop. E-learning can be problematic when students disregard ethical standards and are not honest about them. Academics often find it difficult to deal with. This study aimed to identify the factors affecting academic honesty and their priority at Virtual School, Tehran University of Medical Sciences (ETUMs). Methods: The study employed a survey and factor analysis methodology. In this study, 240 students and teachers from ETUMs were surveyed to assess factors that affect academic honesty among students and teachers, using a questionnaire made by a researcher. The data were analyzed using Principal Components Analysis (PCA), and the Friedman test was used to prioritize the factors. Results: A PCA of survey results found five factors affecting students' academic honesty in E-learning, which explained up to 53.66% of E-learning's honesty total variance. These include socio-cultural (26.30), Metacognitive skills (8.88), Personal characteristics (7.12), motivational (6.07), and instructional factors (5.27). Additionally, Friedman test results indicated that the Metacognitive skills (Mean Rank: 3.58), socio-cultural (Mean Rank: 3.57), instructional (Mean Rank: 3.34), motivational (Mean Rank: 3.13), and Personal characteristics (Mean Rank: 1.38) respectively had the greatest role in student academic honesty from the faculty perspectives. Additionally, instructional factors (Mean Rank: 3.87) are ranked highest from the perspective of students, followed by motivational factors (Mean Rank: 3.43), Metacognitive skills factors (Mean Rank: 3.41), socio-cultural factors (2.81), and Personal characteristics factors (1.48). Furthermore, Cronbach's alpha coefficients indicate reliability (= 0.87). Conclusion: Among the known effective factors, Metacognitive skills and instructional factors were the most important from the teacher and student's perspective. Thus, it is crucial to provide instructional materials that meet students' needs and increase the student's motivation to learn and self-esteem. It is also vital to employ the appropriate teaching methods to ensure the learning of the material and improve the student's attitude and reduce academic dishonesty.