Photodynamic therapy (PDT) is a promising modality, which uses light energy to activate a nontoxic photosensitizer to treat various diseases like cancer and infectious diseases. Hypocrellin B (HB) is a naturally occurring photosensitizer isolated from traditional Chinese medicine Hypocrella bambusea. However, the high hydrophobicity and poor selectivity severely limit its application. Apoferritin, a macromolecular protein, can serve as an attractive nanocage to carry HB while improving its water solubility and tumor selectivity. In this study, novel HB-apoferritin nanoparticles (HB-AFT NPs) were successfully developed by assembling HB within the apoferritin nanocage. The self-assembled HB-AFT NPs have a narrow size distribution and smooth surface with an average diameter of 12 nm and a HB encapsulation efficiency of 85%. The morphological observation and circular dichroism analysis showed that the encapsulation strategy of HB did not impair apoferritin structure, and thus it potentially maintained the tumor targeting ability of apoferritin. Compared with free HB solution, HB-AFT NPs exhibited more pronounced photodynamic activity on MDA-MB-231 cells due to the higher intracellular uptake, increased reactive oxygen species (ROS) production and excellent tumor-targeting. All these results suggest that the self-assembled HB-AFT NPs can be considered as a potential photosensitive drug for tumor targeting photodynamic therapy.