This paper presents an active disturbances rejecter controller (ADRC) for position and path following control of a fully actuated autonomous underwater vehicle (AUV). The unmodeled, undesirable dynamics and disturbances reduce the performances of classical controllers and complicate the design of appropriate and efficient controllers. In the proposed approach, the different modeling complexities; such as uncertain parameters, non-linearities, and external disturbances are considered all as a part of disturbance which is estimated in real-time by the extended state observer ESO, and effectively compensated from the control law. The ESO is also able to estimate the position and velocity of the system in real-time, in case where the full state measurement of the AUV is not possible during experiments. Computer simulations demonstrate the high ability of the AUV tracking control based on ADRC, to follow the desired trajectory in the horizontal plane and space with high precision, and showed high robustness and efficiency in rejecting the external and internal disturbances caused by significant changes in parameters of the system, and the added position disturbances.