The significant trends in the Russian practice of strategic planning are discussed in the article. Therefore, identification of the priorities in the field of science and technology relies heavily on forecasted global data trends, but is not actually embedded in the process of forming the development strategy of socio-economic system (SES) in Russia. Moreover, the rules, by themselves, for selecting priorities and implementing mechanisms have not been substantiated neither methodologically – from the point of adequate understanding of development patterns of SES, nor methodically – according with system diversity in the totality of the current circumstances and factors, relationships and interactions of the SES elements. Such paradoxes have led to a decline both in the quality of the strategy and in the opportunities for its implementation with the purpose to revive science and technology sector, to solve internal problems, to maintain stability and balance of the SES. The paper reviles the specific flaws in the national strategies: discrepancy, fragmentation, inconsistency of the strategy directions both inconsistency of the strategy directions both among themselves and among the sectors of the economy and society. The results of the actual data calculation are presented in the article to illustrate the paradox in choice of some directions in the “Strategy for the Scientific and Technological Development of the Russian Federation” approved on 1 Dec. 2016, so as such choice relies on the so-called “big challenges” of the global world, but not on the internal challenges and opportunities. The key requirements for the strategy were argued in the paper from the perspective of system economic theory, developing under the leadership of G.B. Kleiner in the CEMI RAS. Systemic logic schema to elaborate SES strategy is proposed: from system analysis to synthesize integrated comprehensive image of the future system, based on systemic vision of the problem situation and on systemic assessment of the SES potential in the framework of proposed Structure of conditions and factors. The findings concern fundamental improvements both in practice of elaborating strategy and in developing the theory of strategic planning and governance.