A trajectory control system plays an important role in controlling motions of marine vehicle when a series of way points or a path is given. In this paper, a sliding mode control (SMC)-based trajectory tracking controller for marine vehicles is presented. A small-sized unmanned ship is considered as a control object. Both speed and heading angle of a ship should be controlled for tracking control. The common point of related researches was to separate ship's speed and heading angle in control methods. In this research, a new control law from a general sliding mode theory that can be applied to MIMO (multi input multi output) system is derived and both speed and heading angle of a ship can be controlled simultaneously. The propulsion force and rudder force are also applied in modeling stage to achieve accurate simulation. Disturbance induced by wind is also tackled in the dynamics considering robustness of the proposed control scheme. In the simulation, we employed a way-point method to generate ship's trajectory and applied the proposed control scheme to ship's trajectory tracking control. Our results confirmed that the tracking error was converged to zero, thus demonstrating the effectiveness of the proposed method.