This paper addresses the trajectory tracking of a Vertical Take-Off and Landing (VTOL) aircraft. Our objective is to design a controller for a VTOL aircraft in such a way that the aircraft tracks a predefined 3d spatial path in the presence of constant disturbances and uncertainty in the inertial matrix. Taking advantage of the extraction algorithm, we separate the design for the translational and rotational dynamics. First a virtual controller is designed for the translational dynamics from which the ideal thrust direction is extracted. To deal with the under-actuation of the translational dynamics, we have exploited an auxiliary system while an estimator is also involved in the design of the virtual controller to compensate for the effect of the translational disturbance. In order to keep our estimation bounded, we utilize the projection operator which is also smooth enough. An adaptive sliding mode control is used for rotational dynamics control such that the ideal thrust is accomplished. Since the inertial matrix and the bound on rotational disturbance is unknown, an adaptive structure is used to estimate the unknown bounds. The stability of the control framework is established through Lyapunov analysis. Finally simulation results are given to test the validity of the proposed control scheme.