Operators of unmanned aircraft systems (UAS), performing aeronautical work in accordance with the certification requirements of the Federal Aviation Regulations, are obliged to have a Flight Safety Management System (FSMS), the critical element of which is risk management. The utilization of the risk assessment methods and the development of corrective actions, used in manned aviation, is problematic due to the UAS operational characteristics. The article presents the FSMS methodology for UAS of category B (special category) based on the developments of JARUS group, established with EASA, to address the unmanned aviation operation issues. The proposed methodology integrates the SORA method provisions, developed by JARUS, and comprised into seven documents, into the unified logically related system with consideration to the specific traits of the Russian Federation Aviation legislation and the terminology adopted in the Russian Federation civil aviation. The key problem of assessing the expected effectiveness of risk management actions in the JARUS methodological guidelines does not have a complete solution.The article proposes to solve the problem using professional evaluation by means of the hierarchy analysis method of the fuzzy set theory. This allows us to reasonably build the hierarchy of actions according to their impact on risk mitigation and to classify them into three categories. Such a classification is imperative to evaluate the applicability of actions depending on the amount of total risk. Although the UAS operation of category B is supposed to be performed in the segregated airspace, the methodology takes into consideration not only the risks of collision with objects on the ground but also mid-air collision risks with manned aircraft, since it is usually impractical to create the “ideal” segregated airspace. The proposed methodology can be utilized in the long view when developing risk management practices of UAS operation of category C in open skies.