Benefiting from their unique physicochemical properties, graphitic nanocapsules with a core–shell structure have attracted tremendous interest in bioanalysis and biomedicine recently. Using rational design, various types of graphitic nanocapsules with controllable properties are prepared to meet the demands of different biomedical applications. Graphitic nanocapsules exhibit excellent stability and superior capacity for loading nucleic acids, proteins, small molecules, and drugs due to the large specific surface area of their graphitic shells. Moreover, using the unique Raman bands of graphitic shells with large scattering cross-sections, graphitic nanocapsules are applied in Raman-based detection and imaging. Various types of nanocapsules with superior optical and magnetic properties are available for multimodal imaging applications. By making full use of the intrinsic near-infrared optical absorbance of the graphitic shell and specific metal core, graphitic nanocapsule-based light-mediated therapies are realized, showing superior performance in the killing of cancer cells and pathogenic bacteria, as well as anti-tumor therapeutic efficacy in animal experiments. This review summarizes the synthesis, properties, and functionalization of graphitic nanocapsules and discusses the recent advances in Raman detection and imaging, multimodal imaging, and light-mediated therapy, including concerns related to toxicity. Future prospects of graphitic nanocapsules in biomedical applications are also highlighted.