Recent research results report that extracellular vesicles (EVs) have a central role in both physiological and pathological processes involving intercellular communication. Herein, a simple EVs labeling procedure based on the metabolic labeling of secreting cells (mesenchymal stroma cells, MSCs) with a fluorescein-containing bio-orthogonal dye is described. This procedure was carried out by incubating cells for 72 h with tetraacetylated N-azidoacetyl-d-mannosamine (Ac4ManNAz), a modified sugar containing an azido group that, upon incorporation on the external surface of the cytoplasmatic cell membrane, is specifically conjugated with cyclooctyne-modified fluorescein isothiocyanate (ADIBO-FITC). MSCs released fluorescent EVs did not need any further purification. Finally, cellular uptake and tracking of the fluorescein-labeled EVs were successfully assessed by targeting experiments with MSCs. The method appears of general applicability and it may be very useful opening new horizon on diagnostic and therapeutic protocols exploiting EVs.