Nuclear waste storage materials are inevitable in nuclear industry for preventing the release of radioactive waste products. Glassy carbon has been considered being beneficial to be used in the dry cask needed for nuclear waste storage. Thus, we studied the migration of ruthenium implanted in glassy carbon upon annealing. Our investigations show that ruthenium implantation caused defects in the glassy carbon structure, with more defects observed in the room temperature as-implanted samples compared to those implanted at 200 °C. Annealing the as-implanted samples from 500 to 800 °C showed no significant change in the ruthenium depth profiles, indicating the non-diffusivity of ruthenium in glassy carbon at these temperatures. However, annealing at higher temperatures (from 900 and 1300 °C) resulted in an increase in the maximum depth profile peaks, accompanied by a shift towards the surface, and a decrease in the full-width at half-maximum. These changes indicate the aggregation of ruthenium atoms in the near-surface region. Additionally, more ruthenium aggregation was observed in room temperature implanted samples compared to those implanted at 200 °C. This difference is attributed to the higher concentration of defects in room temperature implanted samples, which promotes ruthenium aggregation. Moreover, the migration and aggregation of ruthenium in the near-surface region contributed to an increase in the surface roughness of the glassy carbon.