Induced pluripotent stem cell (iPSC) derived extracellular vesicles (EVs) constitute a new class of cell-free regenerative medicine. Non-invasive tracking of the delivery and in vivo distribution of EVs is highly desirable. Traditional labeling methods suffer from either low labeling efficiency or difficulty with purification. Here, we report a new labeling strategy using surface-functionalized magnetic particles, in which the nonencapsulated magnetic particles can be easily separated from the labeled EVs, allowing the preparation of magnetically labeled EVs with high purity. We then demonstrate in vivo tracking of magnetically labeled EVs in the kidney and liver using MRI.