This article is dedicated to the system of financial control of the projects of the megascience class in the Russian Federation. The author highlighted the structure of this system, defined the goal, objectives, and principles of financial control of projects of the megascience class, investigated the features of the implementation of external and internal state financial (budget) control of megascience projects. The article concludes that the priority of budget financing for megascience projects in the Russian Federation predetermines the leading role of budget control. The financial control model is also influenced by the organizational and legal form used in the implementation of megascience projects. The article demonstrates that the assignment of the functions of the operator of megascience projects to an international intergovernmental organization or a specially created organization with the distribution of shares among the countries participating in the project, allows to provide more transparency of information on the progress of its implementation in general and financing in particular. The study showed the need for wider application of independent audit control of megascience projects being implemented in the territory of the Russian Federation. Based on the results of the study, proposals were formulated aimed at increasing the efficiency of spending money in the process of implementing megascience projects and the transparency of the activities of scientific institutions with regards to the public.