The Flying-V is a tailless, V-shaped flying-wing type aircraft that promises to offer significant increases in aerodynamic efficiency. Due to its configuration, the Flying-V faces some control and stability related issues. These include limited control authority, pitch break tendencies and non-ideal handling qualities. To enhance the handling qualities of the Flying-V, Incremental Nonlinear Dynamic Inversion (INDI)-based flight control systems have been proposed. INDI, a sensor-based alternative to conventional Nonlinear Dynamic Inversion (NDI), is rooted in the principle of feedback linearization. Unlike NDI, INDI does not depend heavily on accurate on-board models (OBM), thereby offering increased robustness to aerodynamic uncertainties. However, singular perturbations—such as time delays, aeroelastic effects, and additional unmodeled or unknown dynamics—have been identified as challenges for INDI-based control laws. Various strategies have been explored to improve the overall robustness of INDI-based flight control systems, including outer-loop tuning and inversion loop augmentation strategies. In this research a multi-loop µ-optimal approach for designing robust inversion-based flight control laws is explored for the design of an explicit model-following pitch-rate control system for a short-period approximation of the Flying-V’s longitudinal dynamics. The design problem takes into account both regular and singular perturbations. To assess the robust stability and performance of the proposed control systems, a structured singular value analysis was performed. It was concluded that a multi-loop synthesis approach is capable of achieving better robust stability and performance levels when compared to either strictly inner-loop or outer-loop synthesis. As such, it can be concluded that multi-loop synthesis approaches are best capable of leveraging the robustness functionalities of multi-loop inversion-based control systems.