This paper presents an ontology for assessing the intellectual capital of R&D-intensive companies. The obtained results are based on numerous studies of the intellectual capital as the complex phenomenon as well as on the analysis of information uncertainty in research and development process as the basis for innovations. The paper examines the essence of intellectual capital components from the perspective of managerial tasks. The proposed ontology incorporates sub-ontologies of innovation, human, organizational (structural) and relational (social) capital, as well as the mechanism of knowledge extraction. For each sub-ontology there is a description of classes, properties of these classes and relationships (object properties) that form a model of knowledge to support the evaluation of the intellectual capital in R&D-intensive companies. The result can be useful for specialists engaged in the creation of formalized methods and tools for intellectual capital management, as the presented ontology has wide potential for expansion and scaling.