In this paper, a windage loss characterisation strategy for Flywheel Energy Storage Systems (FESS) is presented. An effective windage loss modelling in FESS is essential for feasible and competitive design. Unlike generic aerodynamic loss models, FESS require particular attention to their unique characteristics i.e., vacuum, small airgaps, high angular speed, and presence of low friction rotor supports.The proposed model is based on several analytical and semi-empirical windage loss solutions for cylindrical and planar surface interactions, harmonised to manage the transition between laminar and turbulent flows. Also, the model is enriched by introducing corrections for rarefied gasses, using kinetic gas theory formulation. Therefore, it is possible the reduce the windage overestimation occurring with Navier–Stokes equation solutions for laminar flow. The model is compared to case studies from the literature featuring different boundary and operating conditions, to check consistency of all the harmonised models. A dedicated experimental test-rig is developed to validate the corrections to the model for rarefied gas at different vacuum levels. Then, a non-invasive characterisation approach for FESS windage losses in self-discharge phase is proposed and validated on the test-rig.