The current work investigates the effect of canard geometric characteristics on the performance of a lightweight flying wing Unmanned Aerial Vehicle (UAV), capable of both conventional and Vertical Take-Off and Landing (VTOL) flight. The canards are sized as horizontal stabilizers to enhance the UAV’s longitudinal stability and minimize trimming requirements during cruise. Using a Design of Experiments (DOE) approach and, specifically, the Taguchi method, six canards’ design parameters are investigated on three different levels. These parameters are the sweep angle (Λ), aspect ratio (AR), taper ratio (λ), vertical position in relation to the main wing (vpos), incidence angle (ic), and dihedral angle (Γ). An L27 orthogonal array (OA) is used to investigate the influence of these key design parameters using two performance criteria, namely the Lift-to-Drag ratio (L/D) and the pitching moment coefficient (Cm), at cruise conditions (designated as L/Dcruise and |Cm|cruise). The investigation is conducted by using high-fidelity Computational Fluid Dynamics (CFD) methods for each of the 27 configurations defined by the L27 OA, over a range of angles of attack. Based on the CFD results, two distinct combinations are derived for maximum L/Dcruise and minimum |Cm|cruise using the Signal-to-Noise ratio (SNR) analysis. The optimal design parameter combinations for the two performance criteria are A2B1C1D1E1F1 and A2B2C1D2E2F3, respectively. Finally, the Pareto Analysis of Variance (ANOVA) technique is conducted to define the contribution of each of the six design parameters on the L/Dcruise and the |Cm|cruise. More specifically, ic seems to have the most significant effect on L/Dcruise, whereas Λ is the most important parameter for |Cm|cruise.