The purpose of the article is to discuss the management of science in Russia for its compliance with the principles of lean management. With regard to the management of this area, those principles have a number of limitations, which are objectively due to the weak ability to formalize the processes occurring in it and the highly individualized work of a researcher. The analysis of the main challenges and threats arising in the management of science due to dysfunctional, erroneous management decisions is proposed. Thus, attempts to formalize and institutionalize separate processes often lead only to increasing unproductive losses, especially when it comes to blindly borrowing foreign institutions without a clear analysis of their efficiency. The same applies to the incorrect distribution of responsibilities between research and innovation agents who do not have competencies in the related field.