This Thesis presents the design, development, and validation (through ground and flight testing) of an innovative data acquisition and processing system utilizing optical sensors for real-time health monitoring of aircraft systems and structures. The primary objective is to exploit the capabilities of Fiber Bragg Grating (FBG) sensors, designing the acquisition architecture and the processing algorithms, in order to acquire the FBG raw measurements and transforming them into useful information for flight testing, real-time monitoring and advanced maintenance purposes. The UAV used for this research, Anubi, is a fixed-wing aircraft with an extensive instrumentation setup, including FBG sensors integrated into the wings for strain measurements, along with additional optical sensors for thermal, structural and system monitoring.