Space transportation system uses the liquid hydrogen of the fuel as a coolant of the engine. Therefore, it is necessary to predict the heat flux to the engine wall in high accuracy for efficient cooling with a minimum coolant. However, the prediction of the heat flux to the scramjet engine combustor walls, is quite difficult due to complex interaction of flow and combustion. In this study, a sidewall-compression-type scramjet engine was tested under Mach 6 flight conditions using Ramjet Engine Test Facility. The heat flux was measured using water-cooled heat-flux meters installed on the sidewall within the combustor sections. The experimental results were compared with CFD analysis of the whole engine to predict heat flux distribution on the engine wall. The numerical results of wall pressure distribution showed good agreement with the experimental data. However, the experimental results of heat flux were extremely higher than the numerical results due to the radiation heating which was not considered in the CFD analysis. Based on the results, the average heat flux of the sub-scale scramjet engine with 300 K isothermal walls was 1 MW/m2 in the stoichiometric fuel rate at Mach 6 flight conditions.