The author examines the problem of the development of the regional education system in the context of studying the history of development and integration into the Empire of newly annexed lands and peoples. The research goal is to examine integration processes in the development of the regional system. Comparative-historical, retrospective, and functional methods are used. Based on the documents of the Russian State Historical Archive and published statistical data, the author determines integration manifestations in the field of management of the education system and establishes the role of public organizations in the process of structural integration. The author concludes that general imperial principles and governmental structures were introduced in the education system. The lack of school boards and the university impeded the final integration of the regional education system.