Accurate heat transfer prediction is essential to the design and development of hot structure hypersonic vehicles. Thermo-mechanical compliance is an inherent feature of hot structure hypersonic vehicles, necessitating consideration of fluid-thermal-structural interactions. Additionally, one of the largest sources of uncertainty in heat transfer predictions is the location of boundary layer transition, which itself is associated with a 3 - 8 times amplification of the heat load. This work represents a first investigation into the effect of thermo-mechanical compliance on hypersonic boundary layer stability, with the goal to improve fundamental understanding and reduce uncertainty in the design and development of hot structure hypersonic vehicles. Investigation into the effect of thermo-mechanical compliance on hypersonic boundary layer transition is carried out using the University of Minnesota Stability and Transition Analysis for hypersonic Boundary Layers (STABL) code in conjunction with thermo-structural responses computed from a coupled fluid-thermal-structural analysis of a metallic panel. Several aspects of compliant surface panels are analyzed, namely 1) panel buckling direction, 2) panel location, 3) panel arrangement, and 4) panel response history. Results indicate that panel location has a strong influence on boundary layer stability, and that if arranged properly, thermo-mechanical compliance may delay transition.