The present study aims to explain the model of university transformation in the thought of Imam Khamenei from the perspective of cultural engineering. This research was conducted using a qualitative approach and the thematic analysis method. The analysis population consisted of the Supreme Leader’s statements on the university, from which 48 relevant passages were extracted and analyzed by searching the keyword “university” in the database of the Office for the Preservation and Publication of the Supreme Leader's Works. To enhance the trustworthiness of the findings, strategies including inter-coder agreement, peer debriefing, and member checking were employed. The findings revealed that the model of university transformation comprises one overarching theme (“Transformation in the University”), three organizing themes (“Current Situation of the University”, “Path to University Improvement”, and “Ideal and Desirable University”), and 48 basic themes. Data analysis indicates that the extracted organizing themes conceptually correspond to the three levels of cultural engineering—namely existing culture, target culture, and ideal culture—and that university transformation can be explained as a process of cultural engineering. Furthermore, three interconnected macro-goals of university transformation were identified: the “Islamic University” as a center of religious and moral identity-building, “Iran’s Scientific Authority” as the axis of scientific power, and the “Insightful University” as a socially responsible and awareness-raising institution. The results show that, in Imam Khamenei’s thought, the university is not merely an educational and research institution, but an engineerable cultural system whose transformation begins with understanding the existing situation, proceeds through designing the target culture, and ultimately leads to the realization of the ideal culture. Accordingly, the proposed model can provide a theoretical and practical framework for cultural policymaking in the higher education system of the Islamic Republic of Iran.