In this paper, residual sway control of objects that are moved underwater is investigated. The fuel transfer system in a nuclear power plant transfers the nuclear fuel rods underwater. The research on the dynamics of the loads transferred in different mediums (water and air) and their control methods have not been fully developed yet. The attenuation characteristics of the fuel transfer system have been studied to minimize its residual vibration by considering the effects of hydrodynamic forces acting on the fuel rod. First, a mathematical model is derived for the underwater fuel transfer system, and then experiments have been conducted to study the dynamic behavior of the rod while it travels underwater. Lastly, the residual vibration at the end point is minimized using the input shaping technique.