The gut and skin health are closely related, defined as gut-skin axis. In particular, gut microbiome has been revealed as major factor of gut-skin axis (gut-microbiome-skin axis). Psoriasis, atopic dermatitis, acne vulgaris, rosacea, hidradenitis suppurativa, and alopecia areata are elucidated as skin disease related with gut microbiome. However, in most clinical situations, skin diseases did not show significant improvement with probiotics alone. Because, various factors are involved in gut-microbiome-skin axis, including intestinal permeability, detoxification, brain function, neurotransmitter, immune and inflammatory imbalance. Also, probiotics alone cannot induce significant changes in whole intestinal microbiome. Functional medicine suggests 5R program (or 5R treatment) as a method to restore overall intestinal health. 5R program consists of five steps: remove, replace, reinoculate, repair, and rebalance. In the remove stage, antibiotics such as rifaximin are used to reduce intestinal microorganisms. In the replace stage, digestive enzyme or supplements for gastric or bile acid secretion are used. In the reinoculate stage, probiotics and prebiotics are supplied. In the repair stage, the intestinal barrier is restored by glutamine, lactoferrin or zinc. In the rebalance stage, lifestyle modification is emphasized to maintain balance between gut and whole-body health. It is thought that 5R program is more effective than probiotics alone in skin diseases, but the evidence is still lacking. We present a case of alopecia areata who did not response to conventional treatment but cured after 5R program and nutrition therapy, to explore the effectiveness of 5R program on skin disease with literature review.