This paper describes the numerical and experimental investigation of rigid and compliant hypersonic control flaps undergoing fluid-structure interaction (FSI). The purpose of the study is to investigate experimental techniques that support the evaluation of flight control systems in hypersonic ground test—with the emphasis of providing control to a trailing-edge flap model undergoing FSI. The rigid flap and compliant flap (of 1 mm thickness) were tested at inclination angles of 0°, 5°, 10°, 15°, and 20°. Numerical simulations of two-and three-dimensional flow fields were carried-out in US3D, while the experiments were conducted at the University of Southern Queensland hypersonic wind tunnel facility (TUSQ), under the test flow conditions of Mach 5.8, 75 K and 755 Pa. The forces and moments acting on the models—primarily the lift, drag and pitching moment—were measured with a six component load cell. Tests were carried-out both with and without the load cell to observe the models’ responses independently. The schlieren method was used to visualize the flow fields. The schlieren images were also used to obtain the flap deformation profile, as well as, the flap trailing-edge oscillation response. Frequency analysis of the complaint flaps was performed with the load cell measurement responses of lift, drag and pitching moment, and schlieren-tracked response of the flap trailing-edge. From the analyses, the load cell was found to have a low-frequency response of its own. In absence of the load cell, the compliant flap trailing-edge oscillation induced a new structural vibration mode that lead to a destructive interference of the oscillation. While, in the presence of the load cell, it’s low-rigidity had the effect of damping this induced vibration. The data and analysis presented in this study are also used in designing the future experiments that will implement a software-in-the-loop actuated control of the rigid and compliant flap models.