Background MEBO is an analgesic and antibacterial natural agent. Sesame oil extract plays a positive effect in wound healing that may be attributed to its ability to scavenge free radicals and antioxidant properties. Material and methods In this study, MEBO was topically applied to the site of a traumatic oral ulcer to examine its therapeutic effect on pain relief and wound healing. Patients were randomly assigned into two equal groups: group I (MEBO), group II (control), (n?=?15 patients each). Pain was recorded by using the Visual Analogue Scale (VAS), wound size was measured at days 2, 5, and 10. Cytological analysis was also performed using the superficial epithelial cell and keratinization indices. Results There was a statistically significant difference in VAS scores and wound size between MEBO group and control group (p?≤?0.001). Cytological results of MEBO group showed a highly significant improvement (p?≤?0.00001) in re-epithelization and keratinization indices over time. Conclusion Our results showed that the application of MEBO on traumatic ulcer sites has a significant improvement in wound healing and rapid enhancing effect on the re-epithelialization rate.