Molecularly Imprinted Polymers (MIPs) are polymeric networks capable of recognizing determined analytes. Among other methods, non-covalent imprinting has become the most popular synthesis strategy for Molecular Imprinting Technology (MIT). While MIPs are widely used in various scientific fields, one of their most challenging applications lies within pharmaceutical chemistry, namely in therapeutics or various medical therapies. Many studies focus on using hydrogel MIPs in transdermal drug delivery, as the most valuable feature of hydrogels in their application in drug delivery systems that allow controlled diffusion and amplification of the microscopic events. Hydrogels have many advantages over other imprinting materials, such as milder synthesis conditions at lower temperatures or the increase in the availability of biological templates like DNA, protein, and nucleic acid. Moreover, one of the most desirable controlled drug delivery applications is the development of stimuli-responsive hydrogels that can modulate the release in response to changes in pH, temperature, ionic strength, or others. The most important feature of these systems is that they can be designed to operate within a particular human body area due to the possibility of adapting to well-known environmental conditions. Therefore, molecularly imprinted hydrogels play an important role in the development of modern drug delivery systems.