The modern economy is characterized by a sharp increase in the role of non-material factors (information and knowledge) in ensuring the competitiveness of individual enterprises and institutions, as well as national economies as a whole. Under these conditions, the ability to create, use and increase intellectual capital is the basis for the economic growth of engineering business entities. The main purpose of the study is to model the counteraction to the main threats of intellectual capital for innovation-oriented systems in the engineering sector of the economy. The relevance of the study is given by the fact that the formation and use of technical, economic, industrial, and other types of knowledge, the totality of which forms intellectual capital, is becoming an urgent problem for modern systems tuned to innovative development. The threats to managing the intellectual capital of innovation-oriented systems are now the most significant, since the achievement of the ultimate goals of the system itself depends on the efficiency of the use of intellectual capital. Taking this into account, intellectual capital is becoming a real and valuable target of criminal encroachments today, which requires scientists to form a clear model for countering these goals. The research methodology involves the use of mathematical methods of information support for the process of counteracting the negative impact of threats. According to the results of the study, we presented the modeling process. As a result, a model was built to counteract the main threats of intellectual capital for innovation-oriented systems in the engineering sector of the economy. Further research requires the construction of a mathematical mechanism for responding to new challenges to the intellectual capital management system for innovation-oriented systems.