The processes of globalization and integration in modern conditions have significantly intensified. They have a significant impact on the sphere of education, causing the intensification of the processes of reforming higher education as a single integrated pedagogical system. These trends lead to the need to reformat the purpose, content, methods, means, and forms of education in higher education based on innovation, interaction, and mutual coherence. The article aims to substantiate the theoretical foundations and applied aspects of the study of higher education as a pedagogical system. The methodological basis of the study consists of general scientific and special methods of scientific knowledge and fundamental research, namely: system analysis, synthesis, scientific abstraction, analogies, comparisons, comparative analysis, graphical, tabular, generalization, and systematization. The obtained results of the study helped to establish that the development and functioning of higher education as a pedagogical system in modern conditions of uncertainty and danger is subject to significant destabilizing factors and factors of the external and internal environment, among the most significant of which are the COVID-19 pandemic and the transition of higher education institutions to distance learning. The need for higher education to introduce innovative means of teaching and providing educational services, as well as the formation of conceptual foundations for the strategic development of higher education as a pedagogical system has been revealed. The structural and logical scheme of functioning of higher education as a pedagogical system is proposed, which provides for close interaction of the subjects of the educational process in higher education within the structural and functional components of the pedagogical system. The proposal to strengthen the strategic management of higher education as a pedagogical system has been presented and its main stages have been defined.