In the present study, the challenges and strategies of Iranian higher education in the post-COVID era have been considered. The research approach was qualitative and phenomenological, and accordingly, semi-structured interviews were conducted with 19 samples from two groups of chief executive officer and faculty members. Thematic content analysis method was used to analyze the qualitative data. The results showed that the challenges of the higher education system in the post-COVID era in the form of bipolarity include: (1) social health versus social and cultural harms; (2) globalization versus localization; (3) existing curriculum versus emerging curriculum; and (4) honesty versus academic dishonesty. Also, in this regard, strategies and guidelines such as: (1) facilitate and promote domestic and international cooperation; (2) attracting popular support; (3) use of various teaching methods; and (4) develop the competencies of the faculty members are recommended. Therefore, in Iranian higher education, it is necessary for university management in the COVID-19 era to be prepared to advance its goals, and based on the circumstances, to prioritize the review of educational, research and executive methods.