The article discusses the issues of optimal management of a system composed of multifunctional elements (MFE). From a reliability standpoint, multifunctional elements (MFE) belong to a special class of elements that differ significantly from the classic two-pole “work-fail” elements. In addition to their main function, MFEs have the ability to perform other functions assigned to the system. They are multi-pole elements with multiple operational states, partial failures, and total failure. Systems based on multifunctional elements also have a large number of states, which makes it difficult to quantify reliability, survivability, fault tolerance, and other performance indicators. They have the ability to reconfigure when, in the event of partial failure of elements, it is possible to interchange elements and ensure the continued successful functioning of the system. In order to increase the efficiency of systems consisting of MFEs, the design process raises the problem of optimal configuration and distribution of functions between elements. During the operation of the system, in the event of a complete or partial failure of the MFE, the task of optimally managing the replacement process and interchangeability of multifunctional elements arises. This article presents the results of studies of reconfigurable structure systems based on MFEs and, using specific examples, shows the processes of optimal control of the process of selection, configuration, replacement, and interchangeability of MFEs.