Ionic liquids (ILs) usually refer to kinds of salts with melting point below 100 °C and are composed of definite anions and cations. In recent years, in addition to the field of material engineering, the applications of ILs have been extended to biomedical application. As a solubilizer, skin penetration enhancer, antibacterial agent, and macromolecular stabilizer of poorly soluble active pharmaceutical ingredients, ILs have attracted great attention in the field of pharmaceutical research. Among them, choline-based ILs are very popular in the field of drug delivery due to their biocompatibility, biodegradability, low toxicity or non-toxicity and other characteristics. This article mainly reviews the applications of choline-based ILs formed by choline and organic acid and choline-based ionic liquids-pharmaceutical active ingredients in transdermal delivery, topical delivery and oral delivery.