The Fluid-Structure Interaction (FSI) problem occurs when the dynamics of some movable or deformable structure interacts with the dynamics of any internal fluid. This is the case of a rigid-flexible spacecraft with fuel tank inside it. In the Attitude Control System (ACS) design for this type of spacecraft, a crucial interaction can occur between the rigid motion, the fuel slosh motion and the flexible panels’ motion during translational and/or rotational manoeuvre. Those interactions can change the spacecraft center of mass position damaging the ACS pointing accuracy. In this paper one develops a mathematical model for a rigid-flexible satellite considering the fuel slosh dynamics which is modelled using a common pendulum model which is considered to be unactuated. That model is used to design and compare the satellite ACS by the Linear Quadratic Regulator (LQR), the Linear Quadratic Gaussian (LQG) and the H-infinity methods in order to discuss the advantages, disadvantages and limitations of each method. The control inputs are defined by a transverse body fixed force and a moment about the centre of mass. A comparative investigation of the LQR and LQG methods has shown a significant improvement in the satellite ACS performance of what has been done previously, since it is possible to control, simultaneously, the rigid-flexible motion and the fuel slosh motion. On the other hand, although, the H-infinity controller design is preliminary, it has the advantage of including the uncertainties of the system in the design process, resulting in more robust controller.