For the purpose of fault detection of the primary control surface, real-time estimation of the longitudinal stability and control derivatives of the DURUMI-II using the flight data is considered in this paper. The DURUM-II, a research UAV developed by KARI, is designed to have split control surfaces for the redundancy and to guarantee safety during the fault mode flight test. For fault mode analysis, the right elevator was deliberately fixed to the specified deflection condition. This study also mentions how to implement the multi-step control input efficiently, and how to switch between the normal mode and the fault mode during the flight test. As a realtime parameter estimation technique, Fourier transform regression method was used and the estimated data was compared with the results of the analytical method and the other available method. The aerodynamic derivatives estimated from the normal mode flight data and the fault mode data are compared and the possibility to detect the elevator fault by monitoring the control derivative estimated in real time by the computer onboard was discussed.