This article aims to assess the changes in the HEIs management system elements during the pandemic. The methodology was built on the analysis of management cases of Kyiv National University named after Taras Shevchenko and National University "Lviv Polytechnic". The internal documentation of HEIs management: strategies and development plans, internal documentation of quality management system implementation defining the main challenges of HEIs management were also used for case analysis. Results. It was determined that the pandemic generated significant structural changes in the system of HEIs management caused by changes in students' needs, development, and spread of innovative learning technologies, reduction in the number of international students, closing, merging, and restructuring of universities due to funding cuts. The pandemic has put forward challenges to the core business of higher education in supporting students through a wide range of curricula. These challenges make it much more difficult to implement interactive, person-centered traditional classroom instruction based on years of university experience. To adapt to a long-term pandemic, HEIs require flexible educational methods that will continuously adapt to different stages. COVID-19 led to the activation of long-term pedagogical trends, created a natural experiment to test and evaluate numerous innovations.