The Russian innovation system (RIS) is currently facing internal and external challenges that require its institutional structure to change significantly. Social contexts and rules that innovation system actors (business, academic community, state) find relevant must be taken into account in the transformation process. Therefore, in this article the RIS challenges are considered through an analysis of the functions and dysfunctions of its institutions. The article provides qualitative (based on narratives contained in in-depth interviews with the RIS academic field representatives) and quantitative (based on the Global Innovation Index data) analysis of these functions and dysfunctions. The study reveals the following RIS dysfunctions: low quality of formal institutions and lack of consistency in legal regulation, excessive control over the innovators' activities; selectivity and inconsistency of the state innovation policy(federal and regional); underdevelopment of mechanisms for formation of science and business cooperation; lack of production facilities and capacities, as well as physical infrastructure insufficiency for scaling innovative production; both state and private underfunding of science and innovative developments; the disruption of the mechanisms of reproduction of personnel potential for innovation. It has been established that with the quantitative approach it is possible to identify some RIS dysfunctions. Under the current conditions, dysfunctions overcoming is associated with strengthening the state strategic role while maintaining, developing and stimulating strategic entrepreneurial innovations.