Ionic liquids (ILs), due to their inherent structural tunability, outstanding miscibility behavior, and excellent electrochemical properties, have attracted significant research attention in the biomedical field. As the application of ILs in biomedicine is a rapidly emerging field, there is still a need for systematic analyses and summaries to further advance their development. This review presents a comprehensive survey on the utilization of ILs in the biomedical field. It specifically emphasizes the diverse structures and properties of ILs with their relevance in various biomedical applications. Subsequently, we summarize the mechanisms of ILs as potential drug candidates, exploring their effects on various organisms ranging from cell membranes to organelles, proteins, and nucleic acids. Furthermore, the application of ILs as extractants and catalysts in pharmaceutical engineering is introduced. In addition, we thoroughly review and analyze the applications of ILs in disease diagnosis and delivery systems. By offering an extensive analysis of recent research, our objective is to inspire new ideas and pathways for the design of innovative biomedical technologies based on ILs.