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Extracellular vesicles (EVs) are mediators of intercellular communication through the transfer of nucleic acids, lipids and proteins between cells. This property makes bioengineered EVs promising therapeutic vectors. However, it remains challenging to isolate EVs with a therapeutic payload due to the heterogeneous nature of cargo loading into EVs. In this study, enrichment of EVs with a desired cargo was possible through engineering of the hallmark CD63 transmembrane protein. E‐NoMi refers to engineered CD63 with mCherry on the inside of the EV membrane and a tag (3xFLAG) exposed on the outside of the EV membrane. To facilitate EV loading during biogenesis, cargo proteins, such as EGFP, Cre recombinase and the CRISPR‐Cas nuclease (SaCas9), were fused to a nanobody (Nb) protein with a high affinity for mCherry. FLAG‐tag‐based immunocapture from cell conditioned media allowed selection of cargo‐loaded E‐NoMi‐EVs, and tobacco etch virus (TEV) protease cleavage sites were used to remove the 3xFLAG‐tag from the surface of E‐NoMi‐EVs after capture. For functional payload delivery to recipient cells, the vesicular stomatitis virus G (VSV‐G) fusogenic protein was incorporated into E‐NoMi‐EVs to form fusogenic EV‐based vectors (EVVs) and proved to be 10‐fold more effective at cargo delivery than EVs generated by size‐exclusion chromatography. Functional delivery of cargo with E‐NoMi‐EVVs was validated in two mouse brain models in vivo.