Subject. To grow steadily and successfully, any economy should improve its mechanism for managing the socio-economic development, which should rely upon scientific approaches, methods and mechanisms. Objectives. The study is an attempt to outline the concept for developing the national economic system of innovation through investment engineering. Methods. The study is based on methods of generalization and systems analysis. Results. We propose a new concept for formulating the modern national system of innovation economics, which poses an investment project as the backbone constituent, being performed by diverse entities and organizations. The system raises the probability that comprehensive investment projects will be successfully implemented, including the reliability of mutual settlements for the sake of the ultimate economic effect. Conclusions and Relevance. The investment concept herein opens new opportunities for a new progressive strategy for the national economic development. Based on investment engineering principles, the economic system will carefully protect all types of property, effectively distribute the national property among federal, regional and local entities, and position regional and local budgets as a set of investment projects or the single investment program for the development of regions and country as a whole. The findings help implement new approaches to developing the national economic system of innovation, which will enhance the performance of manufacturing enterprises and public, collective and private entities. It will contribute to the transparency of financial flows in the non-public sector of economy and considerably curb the informal sector of economy.