Professional marginalization in higher education is a hidden but effective phenomenon that can weaken the human capital of the university and overshadow its scientific and social functions. Therefore, the present study examines the roots and psychological-organizational consequences of the phenomenon of professional marginalization in Iranian higher education. A qualitative research approach and an interpretive phenomenological strategy were used. The research participants included 18 professors and academic experts from several public universities who were selected through purposive sampling and theoretical saturation criteria. The data collection tool was an in-depth semi-structured interview. The data were also analyzed using the inductive coding method and MaxQuda 2020 software. The findings showed that professional marginalization in universities is reproduced in institutional structures and culture rather than being caused by individual failure. Centralized bureaucratic structures, a quantified culture and formal evaluation based on points, and a number-based system that ignores the social impact of knowledge are among the most important organizational factors of this phenomenon. These conditions lead to consequences such as a sense of meaninglessness, existential burnout, professional isolation, reduced collaborative interactions, loss of self-confidence, collapse of academic identity, and decline in the social status of academics. In summary, academic professional marginalization is a structural and lived experience in Iranian higher education that requires a rethinking of structures, academic culture, and the evaluation system.