This paper presents a novel analytical method for electro-mechanical design of a high speed long-term flywheel energy storage system and thermal evaluation of possible operating modes of the system. Flywheel's composite shell rotor along with the motor/generator unit are assumed to be placed into a sealed vacuum chamber, which presents a challenge of heat transfer, produced by rotor losses. Developed method takes into account thermal radiation properties of the rotor and is realised using Mathcad software, which allows for quick investigation of any flywheel configuration. The method involves calculations for preliminary rotor sizing and determining achievable operation modes, while keeping the rotor under a specified temperature limit. Results of using this method for studying dependencies of thermal performance on initial system parameters are presented and conclusions are drawn. Based on the conducted study, recommendations on system design considerations are given.