The characteristics of the flow structure and wall shear stress (WSS) in a hydrogen-fueled scramjet were investigated. A microelectromechanical system-based sensor was used for measuring the WSS. The flow structure was found to be stable in both nonreacting and reacting flows. The expansion waves near the cavity step that occurred in a nonreacting flow were transformed to oblique shock waves owing to hydrogen combustion, and the cavity shear layer was lifted into the core flow. The flame was in the cavity shear layer and the wall boundary layer near the top wall. The time-averaged value (TAV) of the WSS in the isolator was about 825.6 Pa, and the flow was turbulent. The intensity of WSS fluctuations was about 21.5%, and the probability density function of the WSS was negatively skewed in a nonreacting flow. The TAV of the WSS decreased from 370 Pa to 269.5 Pa in the combustor after combustion occurred. This was because the velocity gradient was decreased in the combustion flow. The intensity of WSS fluctuations was increased by the hydrogen combustion.