Rational: A bioactive small molecule of precision medicine involves targeted therapies. Shikonin, a herbal extract, is an active small molecule that is traditionally used in wound healing for its anti-tumor and anti-inflammatory properties. Therefore, the present study aims to evaluate the anti-inflammatory role of shikonin in skin burn wound healing and hair follicle regeneration and to identify molecular signaling pathways that promote the regeneration. Method: A secondary skin burn model of mice was established by conventional method. The burn wound was externally treated with shikonin ointment and excipient treated mice were used as controls. Skin samples were taken on the day 3 and 7 after drug treatment and the dosage was unified in the experiments. The wound healing process was observed by histopathological and immunofluorescence (IF) staining. The proliferation of hair follicle cells in wound skin was tracked by 5-Ethynyl-2'-deoxyuridne (EdU) staining. The inflammatory factors at the wound healing site were quantified by polymerase chain reaction (qPCR). The PI3K/Akt, P65, Ki67 signaling proteins and Bax/BCL2 apoptosis proteins were studied by western blot analysis. The functionality of PI3K/Akt signaling pathway was tested using LY294002, an inhibitor of PI3K. Result: Shikonin treated mice group exhibited better and faster skin burn wound healing in comparison with the controls. The proliferation of new skin cells and hair follicle regeneration in the wound site of the shikonin treated group was more active. The recruitment of macrophages in shikonin treated group was inhibited inturn decreased the expression of inflammatory factors. However, LY294002 inhibited the shikonin-mediated PI3K/Akt signaling pathway and affected the wound healing process. Conclusion: In conclusion, this study strengthens the hypothesis that bioactive small molecule, shikonin, inhibits inflammation, promotes wound healing and has a significant protective effect on the deep hair follicles against burn skin injury by activating the PI3K/Akt signaling pathway.