Shikonin is an ointment produced from Lithospermun erythrorhizon which has been used in traditional medicine both in Europe and Asia for wound healing and is associated with anti-inflammatory properties. The goal of this work is to assess the analgesic properties of Shikonin in the CFA-induced inflammation model of pain. Rats were subjected to inflammation of the hind paw by CFA injection with a preventive injection of Shikonin and compared to either a control group or to a CFA-inflamed group with the vehicle drug solution. Inflammation of the hind paw by CFA was assessed by measurement of the dorsal to plantar diameter. Mechanical thresholds were established by means of the Von Frey filaments which are calibrated filaments that exert a defined force. Finally, the spinal cord of the studied animals was extracted to analyse the microglia population through immunohistochemistry using the specific marker Iba-1. Our results show that Shikonin reduces the paw oedema caused by CFA inflammation. Subsequently, there is a concomitant restoration of the mechanical thresholds reduced by CFA hind paw injection. Additionally, spinal microglia is activated after CFA-induced inflammation. Our results show that microglia is inhibited by Shikonin and has concomitant restoration of the mechanical thresholds. Our findings demonstrate for the first time that Shikonin inhibits microglia morphological changes and thereby ameliorates pain-like behaviour elicited by mechanical stimulation.