A subscale, research rocket thrust chamber operating with cryogenic oxygen and hydrogen exhibits self-excited transverse-mode instabilities with amplitudes of more than 80% of the steady combustion chamber pressure (peak-to-peak) for some operating conditions. During unstable combustion, an increase in the integral heat flux into the water-cooled combustion chamber walls of 20–40% with respect to stable conditions was experienced. A model was derived to predict changes in the axial heat flux profile considering only the dependence of flame length on the amplitude of transverse acoustic oscillations. The model predicts an increase in heat flux in the upstream part of the chamber by up to a factor of 7. This drastic increase is in agreement with past observations of rocket engine failures due to instabilities, in which the structural damage is commonly observed on the faceplate and the walls adjacent to the injection plane. The model also predicts a peak increase in integral heat flux of up to about 25%. While falling short of the peak experimental value of 40%, it nevertheless suggests that flame length is the dominant influence on the distribution of thermal loads in this study.