In a view to further study the diffusion properties of glassy carbon for its applicability as a diffusion barrier for fission products found in high-level nuclear waste, glassy carbon samples were implanted with 150 keV Se ions to a fluence of 1 × 1016 ion/cm2 at room temperature. Some of the implanted samples were subjected to sequential isochronal annealing at two temperature regimes (300–700 °C and 1000–1200 °C) for 5 h under vacuum. Raman spectroscopy was used to investigate the structural changes while Rutherford backscattering spectrometry (RBS) was used to monitor the migration of implanted Se. Implantation of Se amorphized glassy carbon resulting in an increase in density (from 1.42 to 2.1 gcm−3). No notable diffusion of Se in the glassy carbon occurred after annealing at the low-temperature regime (300–700 °C). Raman spectroscopy shows that limited recrystallization occurred after annealing at the low-temperature regime. Appreciable recrystallization coupled with some diffusion occurred at the high-temperature regime, 1000–1200 °C. The original structure of glassy carbon was not achieved after annealing at 1200 °C. Diffusion coefficients of 5.9 × 10−20 m2s−1 and 4.79 × 10−20 m2s−1 were obtained for Se in defective glassy carbon at 1000 and 1100 °C, respectively.