This study aims to identify and explain the challenges of crisis management in Iran’s education system using a grounded theory approach. The study is applied in purpose and exploratory-qualitative in methodology. Data were collected through semi-structured interviews with 23 experts and key practitioners in the fields of education and crisis management. Participants were selected using purposive sampling combined with the snowball technique, and data collection continued until theoretical saturation was achieved. Data analysis was conducted through open, axial, and selective coding based on the constant comparative method. Qualitative analysis yielded 120 initial concepts, which were organized into 10 axial categories and ultimately integrated into the core category of “structural–functional inefficiency of crisis management in the education system.” The main categories included lack of infrastructure and equipment, limited financial resources, inadequate crisis management planning, insufficient psychological well-being of stakeholders, weaknesses in online education, increased educational inequality, poor teamwork, low organizational resilience, improper organization, and weak organizational performance. The findings indicate that crisis management challenges in the education system are multidimensional and process-oriented, stemming from the interaction of structural, managerial, educational, and human factors rather than from resource shortages alone. Structural reform, strengthening managerial capacities, and simultaneous attention to technical and human dimensions are essential for improving the effectiveness of crisis management in education.