Proposing the concept of a brain-gut-skin axis has led some researchers to recognize the relationship among brain activity, gut microbiota, and the skin. Hair follicles are skin accessory organs, a previously unnoticed target tissue for classical neurohormones, neurotrophins, and neuropeptides. Some studies have shown a relationship between the central nervous system and hair follicles that an imbalance in the gut bacteria can affect hair follicle density. This review summarizes existing evidence from literature and explores clues supporting a connection linking the brain, gut microbiota, and hair follicles. It amalgamates previously proposed partial concepts into a new, unified concept—the “brain-gut microbiota-hair follicle” axis, —which suggests that modulation of the microbiome via probiotics can have positive effects on hair follicles. This review also explores how preclinical research on hair follicles can propel novel and clinically untapped applications.