Radio electronic systems are classified as complex systems and are characterized by multi-level hierarchical structure in the form of separate units, blocks and modules. Design and manufacture of highly-reliable systems of onboard radio-electronic equipment with long operating life is an important and complex task, as system reliability can be quite difficult to control at all the stages of its life cycle. The aim of this article is to develop the methods that will allow to satisfy the reliability requirements with regard for failure rate of the designed system during operation. There is a restriction of minimum costs imposed for the given reliability levell at each stage of its life cycle. The study employed the methods of control theory, theory of reliability of complex systems, probability and statistical methods of decision making that consider the dynamics of failure rate and the processes of parameter changes during operating life. Bayesian approach was used for evaluating the reliability level and the risk score. The resultant methodology of managing reliability and risks at design, manufacture, and operation stages of complex technical systems allows to minimize the costs. The developed methods are suggested to be used in selecting the optimal management strategy at all stages of complex systems life cycle, when the lack of required data makes it impossible to meet the minimum common costs requirements.