The Fighter aircraft transmission system consists of a light weight, High Speed Flexible Coupling (HSFC) known as Power Take-Off shaft (PTO) for connecting Engine gearbox (EGB) with Accessory Gear Box (AGB). The HSFC transmits the power through series of specially contoured metallic annular thin flexible plates whose planes are normal to the torque axis. The HSFC operates at high speed ranging from 10,000 to 18,000 rpm. The HSFC is also catered for accommodating larger lateral and axial misalignment resulting from differential thermal expansion of the aircraft engine and mounting arrangement. The contoured titanium alloy flexible plates are designed with a thin cross sectional profile to accommodate axial and parallel misalignment by the elastic material flexure. This paper investigates the effect of misalignment on the transmission characteristics of the HSFC couplings. A mathematical model for the HSFC coupling with misalignment has been developed for analyzing the torque transmission and force interaction characteristics. An extensive testing has been conducted for validating characteristics of the designed coupling under various misalignment conditions. With this the suitability of the model adapted for the design iteration of HSFC development is validated. This method will reduce the design iteration cycles of HSFC and can be extended for the similar development of flexible couplings.