In this work, a hardware-in-the-loop (HIL) simulator is designed to diagnose the behavior of an autonomous sailboat as it navigates between waypoints. At its core, the HIL simulator includes the sailboat pilot on an embedded system. The sensor data input to the embedded system is fed by a navigation simulator that takes into account the different forces on the sailboat due to the wind, waves and current conditions. The HIL simulator is then tested for a navigation route from sea trials published in 2014, and the behavior of the automated pilot is compared to its behavior when the vessel is driven by a crew. As demonstrated, the automated system can outperform the man-operated vessel. The tool is also used to diagnose weaknesses in the sailboat autopilot algorithm that can be improved in the future.