Covalent organic frameworks (COFs) have emerged as a distinguished class of porous materials. Owing to their ability to be constructed through covalent bonds involving light elements, such as hydrogen, boron, carbon, nitrogen, and oxygen, COFs offer greater stability and lower cytotoxicity than metal organic frameworks do, addressing critical limitations in in vivo applications. Their unique attributes, such as high surface area, customizable pore sizes, and versatile surface functionalities, make them ideal for various biomedical applications. This review aims to provide an overview of the recent advancements in modern COFs for biomedical uses. First, a variety of methods for the synthesis of COFs are outlined, which ensures their suitability for medical use. Next, we delve into innovative biomedical applications, emphasizing their role in disease diagnostics and therapies. Finally, challenges, such as clinical translation, biocompatibility, and controlled drug release, are critically discussed, providing comprehensive insight into the potential of COFs in revolutionizing biomedical technologies. Overall, this review offers a comprehensive overview of COFs' capabilities and future prospects in enhancing biomedical technologies.