Flywheel energy storage systems (FESS) have a wide range of applications in energy grids and transportation such as load balancing, frequency regulation, power quality improvement, and primary or secondary power supplies. Recently, the adoption of high strength composite rotors has allowed FESS to more efficiently achieve these goals making them viable alternatives to electrochemical batteries, or other storage devices. Similar to the effects of high performance composites, other rapidly evolving technologies, including high-efficiency motors and low friction bearings, have rapidly pushed FESS technology into new applications and expanded possibilities within existing sectors. However, this growth is hampered by limited understanding of passive discharge behavior and losses associated with the primary sources of energy dissipation – air friction, bearing friction, and electrical machine electromagnetic forces. This thesis seeks to characterize these losses and create models which could be used to predict losses in future FESS designs. Additionally, unexpected fretting wear at the bearing-hub interface is discussed along with possible mitigation methods. To characterize the passive discharge losses, empirical models are created from experimental data. Then they are used to quantify the expected passive discharge to each source at velocities from zero to 5,000 rpm, and the related times. It was discovered that motor losses were by far the most significant, accounting for approximately 80% of total losses, followed by mechanical bearing friction, accounting for approximately 17%, and finally air friction at 66 Pa, accounting for 3%. Finally, fretting was discovered at the bearing-hub interface, likely caused by the high vibrational loads from the bearings and motor, and was exacerbated by the vacuum environment of the FESS. This was, in part, mitigated by modifying the bearing assembly to better fix the bearing races in place.