Purpose: Over the past three decades, academic leaders at Islamic Azad University (IAU) have been facing different challenges for the success of the institutions. The purpose of this paper is to identify the challenges confronting IAU academic leaders in managerial positions. Design/methodology/approach: In this qualitative study, questionnaires containing open-ended questions were sent to academic leaders in managerial positions at IAU branches in Iran and the collected data were analyzed using qualitative content analysis. Findings: The results revealed that the main challenges were categorized into two themes: internal and external environmental factors. Internal challenges were sub-categorized into administration and managerial affairs, financial issues, organizational culture, and students' affairs. External challenges were sub-categorized into political, economic, social, and technological factors, and international and national competitions. Research limitations/implications: This study is limited to Iran and IAU academic leaders who worked mainly in high-level and middle-level of managerial positions; therefore, the results cannot be generalized. The key implications are related to applying continuous professional growth through collaborative and qualified development programs. The implications could be appropriate for other higher education institutions in Iran. Originality/value: This is the first attempt to study the challenges confronting IAU academic leaders in Iran. The findings can help IAU academic leaders plan the most appropriate framework for professional academic leadership development programs.