The article explains the methodology and history of establishing applied psychology of education in Russia, singling out three complementary lines in the development of the system: psychology as social practice of education, psychology as methodology for designing variable education and psychology as an ideology for consolidation of society. The author points out that applied psychology of education has altered the social status of psychological profession in the state and society and argues the necessity of developing a paradigm of tolerance to be realized in the federal programme "Formation of sets of tolerant consciousness and prevention of extremism in Russia".