The primary focus of this research is the finite element analysis (FEA) of a multi-layered panel for thermal protection applications referred to as Panel-A. The panel is composed of an aluminium alloy base, a layer of strain isolation pads (SIP) in the middle and silica tiles on the top layer. The research attempts to understand the multi-layered panels’ thermal protection capabilities and structural responses under adverse thermal conditions. The project unfolds into two major phases: design and FEA simulations. In the design phase, eight SolidWorks models have been created for Panel-A having distinct dimensions and geometries. The models are grouped into two sets: four configurations with SIP integration and four without, with the variable tile gap (3-mm gap, 2-mm gap, 1-mm gap, and no gap). The models are analysed using an FEA software. The comprehensive investigation encompasses both thermal and structural loads, providing valuable insights into thermal distribution across different layers and structural responses (stress patterns) to the pressure loads. A thorough comparative evaluation among the eight models has been conducted and models with SIP showed a better result. The design underwent enhancements aimed at achieving a factor of safety (FOS) on all the panel members, ensuring structurally sound configuration. The overarching goal is to create a safer thermo-structural design that meets specific performance criteria for its functionality. This study adds vital insights to multi-layered panel design and the analysis for the thermal protection system applications, with significant implications for aerospace and other sectors seeking effective thermal protection systems.