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<i>Background and Objectives</i>: Endothelial microparticles (EMP) particularly CD31⁺/42⁻/AV⁺, CD144⁺/AV⁺ and CD62e⁺/AV⁺ have been reported as having increased in cardiovascular-related diseases, making them potential biomarkers for endothelial dysfunction. This study aimed to compare these EMPs in patients with hypercholesterolemia and healthy controls and to correlate their levels with endothelium-dependent vasodilation (EDV) assessed via pulse wave analysis (PWA); an established method of assessing endothelial function. <i>Materials and Methods</i>: EMPs from 88 subjects (44 hypercholesterolemia patients and 44 controls) were quantified from whole blood using flow cytometry analysis. Endothelial function was determined using PWA combined with pharmacological challenge. <i>Results</i>: CD31⁺/42⁻/AV⁺ (3.45 ± 4.74 count/µL vs. 1.33 ± 4.40 count/µL; <i>p</i> = 0.03), CD144⁺/AV⁺ (7.37 ± 12.66 count/µL vs. 1.42 ± 1.71 count/µL; <i>p</i> = 0.003) and CD62e⁺/AV⁺ (57.16 ± 56.22 count/µL vs. 20.78 ± 11.04 count/µL; <i>p</i> < 0.001) were significantly elevated in the hypercholesterolemic group compared with the controls, respectively. There was a significant inverse moderate correlation between all circulating EMPs and EDV: CD31⁺/42⁻/AV⁺ (r = −0.36, <i>p</i> = 0.001), CD144⁺/AV⁺ (r = −0.37, <i>p</i> = 0.001) and CD62e⁺/AV⁺ (r = −0.35, <i>p</i> = 0.002). <i>Conclusions</i>: All EMPs were raised in the patients with hypercholesterolemia, and these values correlated with the established method of assessing endothelial function.