The work presented in this research focuses on the design of a robust nonlinear flight control system for a small fixed-wing UAV against uncertainties and external disturbances. Toward this objective, an integrated UAV waypoints guidance scheme based on Carrot Chasing guidance law (CC) is adopted. The designed attitude angles guidance law is applied to the flight control loop. Nonlinear Dynamic Inversion (NDI) awards the flight control system researchers a straight forward method of deriving control laws for nonlinear systems. The control inputs are used to eliminate unwanted terms in the equations of motion using negative feedback of these terms. However precise dynamic models may not be available and that leads to system instability in the presence of external disturbances or model uncertainties. Therefore a modified incremental dynamic inversion (MINDI) is presented to compensate the model uncertainties and increase robustness and system behavior when compared to incremental NDI. Simulation results showed that the MINDI flight control system is robust against wind disturbances and model mismatch which leads to superior path following performance.