Transdermal drug delivery systems (TDDSs) have become immensely popular over the past few years owing to their safe and noninvasive administration of the drugs across the skin. The TDDSs have provided a better surrogate pathway over conventional routes such as skin patches and injections, thereby resulting in superior and easier acceptance by the patients, minimized side effects, and controlled delivery rates. While TDDSs present these advantages, they also come with their limitations, specifically in delivering both small and macro drug molecules that exhibit moderate solubility in water and/or commonly used volatile organic solvents. To subdue this obstacle, ionic liquids (ILs) are being considered as the potential media not only for the syntheses of drugs but also as suitable carriers for the efficient delivery of both small as well as macromolecules. In this particular book chapter, we have discussed the transdermal drug delivery (TDD) of various partially soluble drugs such as acyclovir, anti-inflammatory drugs like diclofenac and ibuprofen, various anticancer drugs, etc., through heterocyclic-based ILs. Moreover, some green routes for ILs syntheses, including fatty acid-based “amino acid ionic liquids” (FAAAE-ILs) and “magnetic surface-active ionic liquid surfactants” (MSAIL), have also been discussed highlighting their function as the potential transdermal drug delivery agent.