Extracellular vesicles (EVs) have excellent biocompatibility and long retention times in the circulation and have consequently been expected to be useful as drug-delivery systems. However, their applications have been limited because of the inability to introduce hydrophobic compounds to EVs without the use of harmful organic solvents. Herein, we developed an organic-solvent-free drug-loading technique based on the host exchange reaction. We demonstrated that the exchange reaction enabled quantitative loading of EVs with highly concentrated (0.1 mM) hydrophobic fullerene derivatives. Fullerene derivative-loaded EVs (EVs/C60) could eliminate cancer cell lines more efficiently than fullerene derivative-loaded liposomes (Lip/C60). Moreover, the photodynamic activity of EVs/C60 was fivefold higher than that of the clinically available photosensitizer photofrin. EVs/C60 could efficiently suppress tumor growth in tumor-xenograft model mice.