The development of the national economy and economic priorities, both in the medium term and in the long term, is determined by the qualitative composition and use of human capital. The current situation is such that the unfriendly actions of other countries and the increasing imbalance of the entire system of relations on the world stage lead to the need to strengthen the internal potential of the country and search for opportunities to ensure competitiveness and sus-tainability, which brings to the fore a detailed study of threats to economic security, as well as clarifying the methodological tools of their analysis for taking prompt response measures. In this article, an attempt is made to systematize and study the challenges of Russia's economic security related to the formation and development of human capital. We developed express tools for economic security issues related to the formation and development of human capital. In the process of studying the problem of differentiation of the countries of the world and the federal districts of the Russian Federation, methods of statistical analysis were used, as well as methods of expert assessments, ranking, rating assessment, generalization, and traditional methods of economic analysis to substantiate the presented method of operational assessment of threats to economic security. It is concluded that the use of the presented methodological tools in practice will allow classifying challenges regarding the most important qualitative characteristics of human capital, as well as using the results obtained for the development of strategies for the development of territories that take into account their specific features of functioning.