Embedded propulsion systems will allow future hypersonic aircraft to reach amazing levels of performance. However, their peculiar small-radius air-intake leading edges pose serious challenges from the aerothermodynamic, design, integration, and manufacturing standpoints. This paper discloses the methodology developed in the framework of the H2020 STRATOFLY project and specifically tailored to support the conceptual and preliminary design phases of future high-speed transportation systems. The methodology implements an incremental approach which includes multi-fidelity design, modelling and simulation techniques. The specific application to the MR3, a Mach 8 waverider configuration with an embedded dorsal mounted propulsive subsystem, is reported. Different alternative solutions have been thoroughly analysed, including five liquid metals as fluids (Mercury, Caesium, Potassium, Sodium and Lithium) and relative wick and case materials (Steel, Titanium, Nickel, Inconel® and Tungsten) and three leading-edges materials (CMC, Tungsten with low emissivity painting and Tungsten with high emissivity painting). The analysis of the heat transfer limits (the capillary, entrainment, viscosity, chocking and boiling limits) carried out for all five fluids and relative compatible materials, together with a more accurate FEM analysis, suggest the adoption of a Nickel–Potassium liquid metal heat pipe completely integrated in a platelet air-intake leading edge made of CMC material. Ultimately, the effectiveness of the adopted solution throughout all mission phases has been verified with a detailed numerical model, built upon an electrical analogy. •Liquid Metals Heat-Pipe solution for hypersonic air-intake leading edge.•Integrated design methodology with multi-fidelity modelling & simulation techniques.•Application to the STRATOFLY MR3 Mach 8 waverider concept.•Nickel–Potassium liquid metal heat pipe in a CMC platelet air-intake leading edge.•Verification of the effectiveness of the solution throughout all mission phases.