This paper presents a controller design process for an aircraft tracking problem when not all states are available. In the study, a nonlinear-transport aircraft simulation model was used and identified through Maximum Likelihood Principle and Extended Kalman Filter. The obtained mathematical model was used to design a Linear–Quadratic Regulator (LQR) with optimal weighting matrices when not all states are measured. The nonlinear aircraft simulation model with LQR controller tracking abilities were analyzed for multiple experiments with various noise levels. It was shown that the designed controller is robust and allows for accurate trajectory tracking. It was found that, in ideal atmospheric conditions, the tracking errors are small, even for unmeasured variables. In wind presence, the tracking errors were proportional to the wind velocity and acceptable for small and moderate disturbances. When turbulence was present in the experiment, state variable oscillations occurred that were proportional to the turbulence intensity and acceptable for small and moderate disturbances.