This article deals with modelling and a flatness-based robust trajectory tracking scheme for a two degrees of freedom helicopter, which is subject to four types of tail rotor disturbances to validate the control scheme robustness. A mathematical model of the system, its differential flatness and a differential parametrization are obtained. The flat filtering control is designed for the system control with a partially known model, assuming the non-modelled dynamics and the external disturbances (specially the tail rotor ones) to be rejected by means of an extended state model (ultra-local model). Numerical and experimental assessments are carried out on a characterized prototype whose yaw angle (ψ), given by the z axis, is in free form, while the pitch angle (θ), which results from rotation about the y axis, is mechanically restricted. The proposed controller performance is tested through a set of experiments in trajectory tracking tasks with different disturbances in the tail rotor, showing robust behaviour for the different disturbances. Besides, a comparison study against a widely used controller of LQR type is carried out, in which the proposed controller achieves better results, as illustrated by a performance index.