Strategic role of geographic information systems (GIS) for the geographical entity is not in doubt, but there are differences in the understanding of what, when and how to teach. The article presents some aspects of the GIS integration in school education in Kazakhstan. An analysis of the scientific and technical literature, teaching practice shows that the use of electronic school atlas in geography lessons and in extracurricular activities significantly expands the scope of learning activities of students and teachers, stimulates cognitive interest, forms the GIS competence of students. The article considers the problem of formation of geo-information competence of the students on the basis of the use of the electronic geography school atlas developed by the author in the context of the requirements of the state standard of education in Kazakhstan. Scientific novelty of our study is that there has been developed an innovative learning tool, that is an electronic school atlas that provides effective school training at geography lessons in school.