Abstract: Hair follicle (HF), one of the skin appendages, has received a lot of attention to be a new target and pathway for drug delivery. The development of hair follicle targeted drug delivery system (HFTDDS) through percutaneous permeation is particularly important for skin diseases derived from HF such as acne, hair loss, and folliculitis for their on-site action. This review describes the structure and physiological function of HF, the microenvironment of HF, and factors affecting HF permeation. Multiple nanoformulations used to improve the HF permeation and technologies to characterize the HF permeation were introduced. The latest advance of HFTDDS based on nanoformulations were systematically summarized and analyzed in the treatment of acne and hair loss. Finally, the challenges of formulating HFTDDS were discussed. The review is expected to provide some ideas and references for developing delivery systems for treating skin diseases derived from HF.