This study presents a numerical implementation of fast nonlinear model predictive control (NMPC) and nonlinear moving horizon estimation (NMHE) for the trajectory tracking problem of a 3 degree of freedom (DOF) helicopter. The motivation behind using the NMPC instead of its linear counterpart is that the helicopter is operated over nonlinear regions. Moreover, this system has cross-couplings that make the control of the system even more complicated. What is more, according to our simulation scenario, the system has a time-varying dynamical model because it has time-varying parameters which are estimated online using NMHE and the extended Kalman filter (EKF) throughout the control. Although NMHE is computationally more demanding, its capability of incorporating the constraints encourages us to utilize NMHE rather than EKF. Two reference trajectories, namely, sinusoidal and square-like, are tracked, and owing to the better learning capability of NMHE over EKF, the NMPC-NMHE closed-loop control framework is able to track both reference signals with more accuracy than the NMPC-EKF control framework, even under parameter uncertainties. Thanks to the ACADO toolkit, the combined average execution time is 4 milliseconds, demonstrating the potential of the proposed framework for real-time aerospace applications using relatively cheaper processors.