A new trajectory tracking control approach for an under-actuated stratospheric airship is proposed. There is a two-level structure of the proposed controller. A low-level controller based on non-linear vectorial backstepping method, with the rigid-body dynamics expressed on vector form, stabilises the attitude and velocity of the airship, while a high-level controller performs guidance and trajectory tracking task in the three-dimensional (3D) space. Furthermore, a control allocation module based on the active set algorithm is incorporated into the low-level controller to optimise the practical control inputs under constraints of actuator saturation. The closed-loop trajectory tracking control plant is proved to be globally exponentially stable through the Lyapunov theory. Finally, simulations show that the vectorial backstepping trajectory tracking controller can achieve desired tracking performances even if the airship is affected by parametric uncertainties and exogenous disturbances.