<p>Boron nitride nanotubes (BNNTs), which are structurally analogous to carbon nanotubes (CNTs) but composed of alternating boron and nitrogen atoms, exhibit unique physical and chemical properties, including superior mechanical strength, chemical stability, and electrical characteristics. These attributes make BNNTs promising candidates for various biomedical applications. Recent advancements in BNNT synthesis highlight key techniques such as ball milling, chemical vapor deposition (CVD), and chemical and physical modifications to enhance biocompatibility and functionality. Toxicological assessments, including both in vitro and in vivo studies, show the context-dependent, dose-dependent, and administration method-influenced biosafety profiles of BNNTs. BNNTs have diverse biomedical applications, including roles in tissue engineering where they enhance material properties, promote cell differentiation, and act as remineralization agents. They also promise as drug carriers, with targeted delivery, imaging, radiotherapy, thermotherapy, gene delivery, and electro-chemotherapy capabilities. Additionally, BNNTs are utilized in biosensors and exhibit antimicrobial activity. By summarizing these recent advances, key opportunities and challenges in the field are identified, paving the way for future research and development of BNNT-based biomedical technologies. This review provides a comprehensive overview of the recent advancements in the synthesis, functionalization, and biomedical applications of BNNTs.</p>