Two-dimensional (2D) nanomaterials (e.g., graphene) have shown to have a high potential in future biomedical applications due to their unique physicochemical properties such as unusual electrical conductivity, high biocompatibility, large surface area, and extraordinary thermal and mechanical properties. Although the potential of graphene as the most common 2D nanomaterials in biomedical applications has been extensively investigated, the practical use of other nanoengineered 2D materials beyond graphene such as transition metal dichalcogenides (TMDs), topological insulators (TIs), phosphorene, antimonene, bismuthene, metal–organic frameworks (MOFs) and MXenes for biomedical applications have not been appreciated so far. This review highlights not only the unique opportunities of 2D nanomaterials beyond graphene in various biomedical research areas such as bioelectronics, imaging, drug delivery, tissue engineering, and regenerative medicine but also addresses the risk factors and challenges ahead from the medical perspective and clinical translation of nanoengineered 2D materials. In conclusion, the perspectives and future roadmap of nanoengineered 2D materials beyond graphene are outlined for biomedical applications.