The study aimed to investigate the constituents of the ethanolic extract of Micromeria fruticosa and evaluate its antimicrobial and burn healing activities and the isolated compound, rutin. The plant was extracted with ethanol and the active constituents were isolated. The antimicrobial activities of the extract and the isolated compounds were assessed. The burn healing potentiality was evaluated in a second-degree burn model on rats. Five compounds were isolated and identified namely, oleanolic acid 3-O-β-D-glucopyranoside, apigenin, tectochrysin, 7,4' dihydroxyflavone7-rhamnoglucoside, and rutin. Noticeable antimicrobial activities of the extract, fractions and rutin, were obtained. These effects could be attributed to the isolated flavonoids and triterpenes compounds. The topical application of the extract or rutin significantly reduced the wound size and improved the skin histology. The molecular docking simulations predicted potential inhibitory interaction between rutin and the active site of IKKβ that could be responsible for blocking NF-κB activation; this could explain the possible mechanism by which rutin enhances the burn wounds healing process. Ethanolic extract, fractions and isolated compound, rutin of M. fruticosa exhibited significant antimicrobial activities. The plant extract and rutin demonstrated high potentialities to heal burns.