Background: Screening of natural compounds for the development of anti-acne treatment agents has been steadily required considering various side effects of acne medications. Objectives: To compare the clinical efficacy, safety and histopathological changes between Lactobacillus fermented Chamaecyparis obtusa (LFCO) and existing tea tree oil (TTO) for the treatment of mild to moderate acne. Methods: Total thirty four patients were instructed to apply 5 % LFCO to the involved areas of randomly allocated side and 5 % TTO extract to the other side twice a day for 8 weeks in a double blind randomized trial. Results: At the final 8 week, both LFCO and TTO sides showed significant reductions for inflammatory acne lesions. However, LFCO was superior to TTO in the degree of improvement and onset time of efficacy. LFCO side also demonstrated improvement for non-inflammatory lesions, decreased size of sebaceous glands, and sebum output reductions. Protein expressions of NF-κB decreased earlier in LFCO side, and those of IL-1α, IL-8, IGFR-1, and SREBP-1 decreased subsequently. Messenger RNA expressions showed consistent patterns. HPLC-MS analysis further demonstrated that contents of dihydrobenzoic acid, taxifolin 3-O-β -D-xylopyranosid, and quercetin 3-rhamnoside are increased in LFCO. Conclusion: LFCO was more effective and safe for treating various acne lesions compared with existing TTO. Experimental results partly elucidated related molecular mechanisms.