The effect of sequential isochronal annealing on the diffusion behavior of implanted xenon in glassy carbon is reported. Glassy carbon substrates were implanted with 200 keV xenon ions to a fluence of 1 × 1016Xe+cm−2. The sample was annealed in vacuum at temperatures ranging from 300 °C to 1000 °C for 5 h in steps of 100 °C. The RBS depth profiles obtained at temperatures above 800 °C showed that some diffusion occurred. The broadening of the peaks was not accompanied with a loss of the implanted Xe. Microstructural changes in the glassy carbon substrate due to Xe bombardment and annealing were monitored using Raman spectroscopy. The Raman spectrum obtained after xenon bombardment showed that the glassy carbon substrate became amorphized. However, a slight recovery of the glassy carbon structure was noticed after heat treatment. The SEM micrographs of the glassy carbon substrate showed an increase in the surface roughness of the glassy carbon substrate after implantation. The increase in the roughness of the glassy carbon substrate was attributed to the sputtering of the loosely bonded carbon atoms along the polishing marks after implantation and annealing.