In recent years, the concept of autonomous navigation systems has gained substantial significance, with the potential to change the traditional concept of autonomous navigation. The presented numerical simulation investigates the feasibility of a ship’s autonomous navigation system through a laser communication infrastructure handled by a two-degrees-of-freedom (DoFs) acquisition, tracking and pointing (ATP) system able to enable ship–satellite data transmission. The methodology introduced presents the geometrical and kinematic delineation of the model, coupled with the implemented control system, aimed at assessing the pointing accuracy. The minimum requested pointing accuracy is 100 µrad and the analysis highlights the need of using methodologies to reduce the pointing error. Two approaches are investigated to examine a possible improvement of the system, and results show that the pointing phase is influenced less by ship motions and more by errors that occur during the satellite’s positioning and the ship motion acquisition process. A trade-off in choosing parameters to improve the system’s accuracy leads to a satellite’s first targeting time of 0.25 s alongside the probability of hitting the target once every 0.0013 s. The reliability of the system is evaluated through a brief sizing of the optical electromechanical component of the system using the trade-off parameters chosen to improve the pointing phase accuracy.