The article is concerned with a unique and extremely sophisticated process of higher education system functioning under conditions of national conflict and enemy’s occupation of a large part of the state. Documents and events connected with maintaining activity of higher education institutions are analyzed. Three levels of development of this process are considered. They are central (all-Soviet Union and republican), regional (the case of Irkutsk region), and object-related (the case of Irkutsk higher education institutions). Basic aspects of early war period are considered. They are specific features of calling to arms higher education institutions’ employees, graduates and undergraduates specific nature of admission under condition of large scale German offensive and occupation of a large industrially developed part of the state arranging military training for both employees and students speeding up graduation of senior students and reduction of curriculum (up to 3–3,5 years) revising curriculum and its content according to defense needs.

A number of issues of first academic year during the war (1941/42) are also analyzed. They are specific features of adapting teaching staff evacuated from occupied territories and capitals (Moscow and Leningrad) temporary expropriation of educational buildings and classrooms and their usage for defense needs, hospitals, accommodation of evacuated people and teaching staff accommodating wounded by employees and students of the institute of medicine and other institutes results of voluntary donations of different kinds (i.e. money, state loans, warm clothes) of institutes’ employees and students to defense and army field forces needs.