This paper develops general theoretical results about an input–output model-following methodology for linear systems, as an optimal control problem. A control law is obtained by minimizing a quadratic index that takes into account the matching errors and the control inputs. The control is obtained from the Lagrange multiplier method and can be interpreted as an extension of the linear quadratic regulator, with finite and infinite horizon formulations. The major contribution of the paper is the development of solutions involving plant output feedback. The method is illustrated with an application to a nonlinear flexible aircraft with nonstationary aerodynamics and nine flexible modes. Simulations compare state and output feedback solutions. In the proposed example, when taking into account unmodeled flexible dynamics and parametric uncertainties, the best results are given by the proposed output feedback.