Heat losses caused by the operation of compressor units are a key problem in the energy efficiency improvement of the natural gas compression station operation. Currently, waste heat recovery technologies are expensive and have low efficiency. One of these technologies is organic Rankine cycle (ORC) which is often analyzed in scientific works. In this paper, the authors decided to investigate another technology that allows for the usage of the exhaust waste energy—the supercritical Brayton cycle with CO2 (S-CO2). With a thermodynamic model development of S-CO2, the authors preformed a case study of the potential S-CO2 system at the gas compressor station with the reciprocating engines. By comparing the values of selected S-CO2 efficiency indicators with ORC efficiency indicators at the same natural gas compression station, the authors tried to determine which technology would be better to use at the considered installation. Investigations on parameter change impacts on the system operation (e.g., turbine inlet pressure or exhaust gas cooling temperatures) allowed to determine the direction for further analysis of the S-CO2 usage at the gas compressor station. When waste heat management is considered, priority should be given to its maximum recovery and cost-effectiveness.