This paper presents an output-based command shaping (OCS) technique for an effective payload sway control of a 3D crane with hoisting. A crane is a challenging and time-varying system, as the cable length changes during the operation. The OCS technique is designed based on output signals of an actual system and reference model, does not require the natural frequency and damping ratio of the system, and thus can be utilized to minimize the hoisting effects on the payload sway. The shaper was designed by using the derived non-linear model of a 3D crane. To test the effectiveness of the controller, simulations using a non-linear 3D crane model and experiments on a lab-scale 3D crane were performed and compared with a zero vibration derivative (ZVD) shaper and a ZVD shaper designed using an average travel length (ATL) technique. In both the simulations and the experiments, the OCS technique was shown to be superior in reducing the payload sway with reductions of more than 56% and 33% in both of the transient and residual sways that were achieved when compared with both the ZVD and the ATL shapers, respectively. In addition, the OCS technique provided the fastest time response during the hoisting. It is envisaged that the method can be very useful in reducing the complexity of closed-loop controllers for both tracking and sway control.