The questions of further implementation of the operating system software means for the real-time FPGA-based self-configurable computer systems support will be discussed in the paper. These computer systems compete with other types of high-performance computer systems due to high speed characteristics of modern field-programmable gate arrays (FPGAs) — hardware base of reconfigurable computing environment (RCE), and due to advances in design technology of application-specific processors to be synthesized in RCE. Moreover, in the self-configurable computer systems (SCCS) the labor-intensive and time-consuming works of tasks distribution between the processing units and development of the IP cores required for implementation in the RCE, are fully automated and replaced from the operator to the computer system. Taking into account the necessity of further improvement of computer means performance and expansion of reconfigurable devices application in the Cloud Computing and Cyber-Physical Systems (CPS), further development in the field of self-configurable computer systems is a topical challenge of scientific research and engineering.