In recent years, energy-storage systems have become increasingly important, particularly in the context of increasing efforts to mitigate the impacts of climate change associated with the use of conventional energy sources. Renewable energy sources are an environmentally friendly source of energy, but by their very nature, they are not able to supply the required amount of energy in a uniform distribution. This study evaluated the economic efficiency of short-term electrical energy storage technology based on the principle of high-speed flywheel mechanism using vacuum with the help of an innovative approach based on life cycle cost analysis (LCC). The innovative potential of high-speed flywheel energy storage systems (FESS) can be seen in increasing the reliability of the electricity transmission system with the possibility of providing control power to compensate for residual loads caused by volatile renewable power sources and power sinks. Based on the research conducted, the LCC method was selected in this study as the most appropriate method to evaluate the economic efficiency of a high-speed FESS used to compensate for short-term fluctuations in an upgraded electric transmission system. As a result, the adjusted LCC per MWh values were compared with the average intra-hour margin realisable in the Intra-Day OTE Market, while the margin calculation also considered the efficiency of the inertial storage. Under the modelled technical and economic conditions, it was found that a high-speed FESS project that can compensate for short-term fluctuations in the electricity transmission system can be economically efficient in the Czech Republic.