Purpose This study aimed to evaluate the effects and mechanisms of action of royal jelly (RJ) and propolis in an animal model of oral mucositis (OM).Methods Seventy-two male Wistar rats were randomly allocated to four groups (n = 18): control (no treatment), PBMT (intraoral laser, 6 J/cm2), RJ, and propolis. On days 0 and 2, animals received injection of 5-fluorouracil (5-FU). The buccal mucosa was scratched (days 3 and 4) and the treatments were initiated on day 5. Six animals of each group were euthanized on days 8, 10, and 14. Phytochemical analysis (thin-layer chromatography-TLC), clinical, histopathological, immunohistochemical of pS6, pAKT and NF-κB and oxidative stress markers were also investigated.Results TLC revealed the presence of large amounts of sucrose (Rf 0.34) in RJ and flavonoids in propolis. On day 8, lower clinical OM scores (and day 10) and morphological were observed in the PBMT, RJ and propolis groups (p < 0.05). On day 8, immunoexpression of pS6, pAKT and NF-κB was increased when compared to control. On day 14, GSH antioxidant levels were increased in the propolis group compared to control (p < 0.05).Conclusions Our results showed that RJ and propolis, as well as PBMT, are effective in the treatment of OM. The RJ and propolis may explain their excellent wound healing activity and anti-inflammatory effects. Considering that not all patients who develop OM have access to PBMT, the present study demonstrated that topical application of RJ and propolis may be an important alternative for the treatment of OM.