Abstract: This article provides the research results of the economic peculiarities of large-scale scientific mega-class projects. The main features of scientific megaprojects and their difference from the ordinary mega-class projects are considered. The author examines the risk characteristics in implementation of the scientific megaprojects, specificity and problems of management with allowance for risk. The article provides the systematization of the types of risks and measures on their minimization, as well as recommendations for the pre-project analysis of the problem or risks substantiated by the internal and external factors affecting the systemic sustainability of a project. The author presents a new methodological approach for assessing the risk factors, which is based on perceiving megaproject as an unbalanced system of stochastic nature. Presence of a high number of risks accompanying the implementation of the large scientific projects requires its precise identification, distribution of responsibility, as well as a certain set of methods for analyzing risks. The shift of technological and financial risks towards the nongovernment participants of megaprojects in terms of the public-private partnership will allow considering the interests of all participants, including the interests and mission of megaproject itself.