A subsea shuttle tanker (SST) concept for liquid carbon dioxide transportation was recently proposed to support studies evaluating the ultra-efficient underwater cargo submarine concept. One important topic is the position keeping ability of SST during the offloading process. In this process, the SST hovers above the well and connects with the wellhead using a flowline. This process takes around 4 h. Ocean currents can cause tremendous drag forces on the subsea shuttle tanker during this period. The flow velocities over hydroplanes are low throughout this process, and the generated lift forces are generally insufficient to maintain the SST’s depth. The ballast tanks cannot provide such fast actuation to cope with the fluctuation of the current. It is envisioned that tunnel thrusters that can provide higher frequency actuation are required. This paper develops a maneuvering model and designs a linear quadratic regulator that facilitates the SST station-keeping problem in stochastic current. As case studies, the SST footprints at 0.5 m/s, 1.0 m/s, and 1.5 m/s mean current speeds are presented. Numerical results show that the designed hovering control system can ensure the SST’s stationary during offloading. The required thrust from thrusters and the propeller are presented. The presented model can serve as a basis for obtaining a more efficient design of the SST and provide recommendations for the SST operation.