In this study, we evaluate the role of lee waves for the dissipation of transient mesoscale eddies in the Southern Ocean using a 1/10° eddy-resolving model and linear lee wave theory. The results show that the energy dissipation of the total flow due to lee wave generation exceeds its dissipation due to turbulent bottom boundary layer drag, accounting for 0.25 TW and 0.07 TW respectively, and that lee waves make a stronger contribution to the dissipation of transient eddies (0.18 TW) than to the dissipation of the time-mean ACC (0.07 TW). We find that the lee wave generation by transient eddies is also more sensitive to the anisotropy and orientation of small-scale topography than the wave generation by time-mean flows. Our results imply that lee waves should be parameterized in the eddy-resolving ocean models in order to improve the modeled eddy and mixing representation in the Southern Ocean and hence the response of the Southern Ocean to changes in winds.