An adaptive control algorithm using input-output information is proposed for designing an aircraft fault tolerant control system. An input-output model is derived on the basis of a discrete state-space system. The formulated input-output model has the same structure as the autoregressive moving average (ARMA) model does, and therefore, the conventional system identification method using recursive least square can be used to identify the system. To design a reconfigurable control system, an LQ tracker with output feedback scheme is adopted. During the recursive adaptive control process, the system model is updated periodically. The proposed algorithm is applicable to time-varying systems in real time. To validate the performance of the proposed adaptive fault tolerant control technique, numerical simulation of the high performance aircraft with control surface damage was performed.