The development of large-scale supersonic aircraft has always been challenging as numerous problems exist in control, aerodynamics, handling, propulsion, and structural design. The difficulty of these problems increases when designing small-scale supersonic aircraft, and their successful development has remained elusive. In this thesis the flying and handling qualities of a Small-scale Supersonic Uncrewed Aerial Vehicle (SSUAV) are analyzed with the purpose to facilitate future SSUAV design and experimental testing. For this goal, the flying qualities of an experimental Multipurpose Uncrewed Fixed-wing Advanced Supersonic Aircraft (MUFASA) SSUAV under development at the University of Calgary are assessed. Aerodynamic coefficient data is obtained, and a Newtonian mathematical model is created to facilitate the simulation and evaluation of the MUFASA SSUAV. The flying qualities of the MUFASA SSUAV are evaluated against existing crewed aircraft standards. Specifically the Froude scaling method is used as it provides a way to quantitatively compare small-scale vehicles to existing full-scale vehicle standards. The results obtained show that the handling characteristics of the MUFASA SSUAV are acceptable at transonic cruise conditions, however, the aircraft is laterally unstable. A continuous handling quality evaluation was proposed and implemented across the SSUAV’s flight regime providing observations that were unknown in the literature. The results highlight that the mean handling qualities of the targeted SSUAV range from acceptable to controllable in the supersonic flight regime and acceptable in the subsonic regime. Finally, a modified MUFASA SSUAV was compared to other small-scale UAVs as well as full-scale supersonic aircraft where it exhibited much higher roll-rates, leading to the conclusion that SSUAVs pose unique handling quality challenges that need to be addressed.