Experiments and computational analysis have been conducted to study instabilities in the boundary layer over a swept fin–cone geometry in hypersonic flow. Experiments were carried out at the United States Air Force Academy’s Mach 6 Ludwieg Tube. Infrared thermography was employed to assess the surface temperature distribution, particularly the thermal striations on the fin that indicated a crossflow-dominated transition. Increasing the unit Reynolds number increased heating and moved the crossflow-transition front closer to the fin leading edge. Stability analysis based on the linear parabolized stability equations identified unstable stationary crossflow modes across the range of tested unit Reynolds numbers, and the most amplified disturbances were found to have wavelengths of 2–4 mm. The experimentally observed thermal striations were analyzed and found to have initial wavelengths of 2–5 mm but eventually formed higher-amplitude structures with a wavelength of approximately 10 mm. Discrete roughness elements of different diameters and spacings were implemented near the fin leading edge. Boundary-layer transition onset was found to be delayed with a subsequent lowering of the fin surface heating, with discrete roughness elements having a wavelength of 13.33 mm.