The bearings of a flywheel energy storage system (FESS) are critical machine elements, as they determine several important properties such as self-discharge, service life, maintenance intervals and most importantly cost. This paper describes the design of a low-cost, low-loss bearing system for a 5 kWh/100 kW FESS based on analytical, numerical and experimental methods. The special operating conditions of the FESS rotor (e.g., high rotational speeds, high rotor mass, vacuum) do not allow isolated consideration of the bearings alone, but require a systematic approach, taking into account aspects of rotor dynamics, thermal management, bearing loads and lubrication. The proposed design incorporates measures to mitigate both axial and radial bearing loads, by deploying resilient bearing seats and a lifting magnet for rotor weight compensation. As a consequence of minimized external loading, bearing kinematics also need to be considered during the design process. A generally valid, well-structured guideline for the design of such low-loss rolling bearing systems is presented and applied to the 5 kWh/100 kW FESS use case.