Motivation for the investigation of position and waypoint controllers is in demand for Wave Adaptive Modular Vessel (WAM-V) capable of fulfilling various useful applications. Hence, this paper deals with the development of a GPS based position control system for WAM-V able to navigate between waypoints. A waypoint guidance algorithm is discussed with the double loop feedback controller. The outer loop is fuzzy reasoned and generate the desired heading. The inner loop is a PID controller with thrust allocation command. This control design greatly simplifies the control design process and easily applied to underactuated catamaran vessel WAM-V. The fuzzy reasoning fairly represents the behavior and decision making almost like human operator. Based on the manoeuvring experiments, the lookup table is developed for thrust allocation. The WAM-V is equipped without rudder, thus it is driven by a combination of different thrusts to control both speed and heading. The proposed control scheme performed well in the experiments and using that experimental data simulation is improved. The obtained results affirmed that the fuzzy waypoint guidance control algorithm is powerful to realize the autonomous navigation path planning.