The information society places requirements on the profile of graduates, what is unreachable in the inertial education system. We aim for key changes in STEM education at primary and secondary schools through a national wide-impact project IT Academy. Active learning focusing on conceptual understanding and development of selected inquiry skills, together with formative assessment, form our didactic basis for innovation. The development of scientific literacy and computational thinking are also stimulated by changes in the content of science and mathematics curricula. We create a strong link to informatics concepts and practical use of informatics in everyday life, study, work and research. We expect the interest of young people to study computer science and STEM will increase. In this paper, we introduce key concepts of STEM education innovation, with examples of educational activities. The results of the pilot verification are formulated in recommendations to the educational professionals.