It was found that in the 50-60s of the XIX century the opposition of authoritarian and autonomous tendencies of development of university education aggravates. As a result of the positive reform of higher education for educational institutions and the approval of the democratic statute of 1863, the performance of the university’s scientific function, serving the interests of society, and the level of academic freedoms increased. Reactionary activists saw a threat in expanding the powers of professorial boards (M. Hiliarov-Platonov, M. Katkov, M. Liubymov, V. Puryshkevych and others). Progressive professors (in particular O. Walter, O. Kovalevskyi, V. Modestov and others) advocated the preservation of the autonomous provisions of the statute of 1863.The process of restoration of university autonomy in 1861–1882 is covered. Organizational autonomy in Kharkiv Imperial University is characterized. Thus, the board of the institution developed regulations for students and outsiders, rules of the university court, instructions of the student inspector, rules on scholarships and financial aid, rules on the use of textbooks, rules on testing applicants’ knowledge, rules of student control, projects on faculty division to the branch. The effectiveness of faculty meetings has increased. There was an improvement in the quality of departments; the scientific achievements of applicants for vacant positions were analyzed in detail. The council also filed a petition with the ministry to increase the salary of an associate professor.The academic autonomy of Kharkiv University is analyzed. Professors’ lectures became interesting for students due to the attraction of best practices. Teachers constantly underwent scientific internships abroad. A catalog of books was prepared for the library, the funds were constantly replenished due to works published in the university printing house. Cooperation with secondary schools in the district was close.The analysis of organizational autonomy of Kyiv University of St. Volodymyr (council meetings discussed draft legislation proposed by the ministry; approved decisions on reading special courses for students, allocating funds for laboratory equipment, filling vacancies, reviewing student work, etc.). It is also interesting that the minutes of the meetings were published in the “University News”.It is proved that the academic autonomy of Kyiv University was characterized by the strengthening of academic freedoms, educational activities of teachers, providing assistance to low-income students, conducting charitable events. The growth of independence could not go unnoticed by the authorities, which was embodied in the relevant regulations.