AbstractIntroduction: Presenting the existing challenges in e-learning is necessary for increasing concentration, suitable prediction and investment, preparation of effective programs in the learning system. We aimed to assess the pedagogical challenges (instructing and learning) in the development of e-learning in the educational system of Shahid Chamran University of Ahwaz.Material and methods: In this qualitative and quantitative study, 163 faculty members from the mentioned university were selected using the random sampling method. Data were collected through interviews and with the help of questionnaires prepared by the researcher. The questionnaire's reliability (0.92) and validity were confirmed by related experts. Descriptive and inferential statistics were used as appropriated.Results: We found that evaluation, resource management, program management, communication tools, learner-based education, and flexibility were significantly effective on pedagogical (instructing and learning) challenges in the e-learning program at Shahid Chamran University. The mean values for the mentioned factors were 3.70, 3.69, 3.56, 3.43, 3.37, and 3.20, respectively.Conclusion: A combination of the mentioned factors shown to be effective on e-learning for higher education.