Higher education institutions (HEIs) are critical centers for knowledge creation, innovation, and societal development. Crises, including pandemics, natural disasters, political unrest, and financial shocks, pose significant challenges to their administration. Effective crisis management in HEIs requires proactive leadership, strategic planning, communication, and resource allocation to ensure academic continuity, staff and student safety, and institutional resilience. This paper explores theoretical frameworks and practical strategies for managing higher education institutions during crises. It discusses leadership models, decision-making processes, digital transformation for academic continuity, financial and operational management, and stakeholder engagement. Lessons from global experiences, including the COVID-19 pandemic, are examined. Policy recommendations focus on building adaptive capacities, integrating technology, promoting institutional flexibility, and enhancing accountability to sustain HEIs’ educational, research, and societal missions under crisis conditions.