For healthcare, the medicinal plant has become a significant global resource. The United Nations Organization considers that almost eighty percent of the global population uses a traditional healthcare system as the primary means of healthcare. Increased demand, over-harvesting from the wild, natural habitat destruction through land development and agriculture have created serious threats to many medicinal plant species. Furthermore, conventional soil production of various medicinal plant species often results in variably concentrated amounts of bioactive compounds within the individual species as well as significant reduction of species growth. Hydroponic cultivation provides a sustainable method to produce medicinal plants which may provide both increased biomass and increased accumulation of secondary metabolites. The aim of this Comprehensive Review is to provide detailed evaluations of current hydroponic systems available for developing and cultivating medicinal plants, with particular emphasis on how to determine which hydroponic system is applicable for each organ of the medicinal plant including: roots, leaves, flowers, fruits, and rhizomes. This article is divided into sections that analyze the Deep Flow Technique (DFT), Nutrient Film Technique (NFT), Floating Technique (FT), Ebb and Flow, and Solid Media cultures in terms of their effective use in producing each type of medicinal plant. Other new methodologies and technologies, such as using the precursors for secondary metabolite accumulation, elicitor treatments (stimulus for secondary metabolite production), and root exudate harvesting are also discussed as they may potentially facilitate new methods of cultivating high-quality medicinal plants. Finally, while hydroponic cultivation has shown considerable potential for producing many high-quality medicinal plants with increased concentrations of bioactive compounds, there has been little research on whether hydroponic cultivate methods are economically feasible; therefore, future studies need to investigate the economic viability of the use of hydroponic systems for growing medicinal plants.