Hemoglobin (Hb) E/β-thalassemia has a wide spectrum of clinical manifestations that cannot be explained purely by its genetic background. Circulating extracellular vesicles (EVs) are one factor that likely contributes to disease severity. This study has explored the differences in protein composition and quantity between EVs from HbE/β-thalassemic patients and normal healthy individuals. We used Tandem Mass Tag (TMT) labeling mass spectrometry to analyze the EV proteins isolated from the plasma of 15 patients compared to the controls. To reduce biological variation between individuals, the EV proteins isolated from randomly assigned groups of 5 HbE/β-thalassemic patients were pooled and compared to 5 pooled age, and gender-matched controls, in 3 separate experiments. Alpha hemoglobin stabilizing protein had the highest fold increase. Catalase, superoxide dismutase, T-complex proteins, heat shock proteins, transferrin receptor, ferritin, and cathepsin S were also up-regulated in thalassemic circulating EVs. Importantly, haptoglobin and hemopexin were consistently reduced in patients’ EVs across all data sets, in keeping with the existing hemolysis that occurs in thalassemia. The proteomic data analysis of EVs samples isolated from 6 individual HbE/β-thalassemic patients and western blotting results corroborated these findings. In conclusion, we have successfully identified consistent alterations of protein quantity between EVs from HbE/β-thalassemic and normal individuals. This work highlights haptoglobin, hemopexin, and cathepsin S as potential clinically relevant biomarkers for levels of hemolysis and inflammation. Monitoring of these plasma proteins could help in the clinical management of thalassemia.