When an autonomous underwater vehicle is performing missions in the ocean, it is often subject to external disturbances, such as sea currents and changes in salinity. These phenomena can degrade the performance of the controller of the vehicle, which can increase the tracking error or cause instability. Taking into account these issues, in this article, we design an adaptive controller based on high-order sliding mode control and focus on the paradigm of the trajectory tracking of underwater vehicles. First, we rewrite the classical representation of the underwater vehicle in terms of the known dynamics, and then transform it into a control affine structure. Then, we design an adaptive high-order sliding mode controller for trajectory tracking. Also, we prove the stability of the resulting closed-loop system using Lyapunov arguments. Finally, real-time experiments are performed to validate the proposed methodology, as well as its robustness.