Anti-sway control systems are valuable tools for cranes to prevent unexpected payload sway and undesired motion. However, for shipboard cranes, where the operator moves with the ship, anti-sway control systems can result in significant relative motion between the payload and operator, particularly in rough seas while attempting to align the payload with an ocean-frame target. Therefore, an important question to ask is, do operators actually find anti-sway systems intuitive, or do they feel they have to “fight” the system to achieve their desired performance? To address the question, this paper presents a human factors study designed to evaluate the effectiveness of a shipboard crane anti-sway system with an operator-in-the-loop. Participants completed a series of tests in a virtual-reality simulator, in which they attempted to align the payload of a nine degree-of-freedom shipboard knuckle boom crane with targets in both the ocean/world coordinate frame and ship deck coordinate frame, using an anti-sway system that provided complete motion compensation in both coordinate frames. The study found that there was a statistically significant improvement in the participant’s ability to track a desired payload target with the use of the anti-sway system of up to 49.1%. In addition, as the participant had no knowledge of how the anti-sway system operated, or even if it was active, the results indicate anti-sway control systems can be intuitive for operators to use.