The aim of the present study was to assess whether different functional virgin olive oils (FVOOs) with varying phenolic compounds (PC) could protect the plasmatic fat-soluble vitamins, which in turn could improve the endothelial function. In order to select the optimal phenolic dose in the improvement of ischemic reactive hyperemia (IRH), a dose-response study (n = 12, healthy subjects) was performed and the enrichment of 500 mg PC/kg oil was selected. In a 3-week cross-over sustained study (n = 33 hypercholesterolemic subjects), the consumption of 25 mL/day of two phenol-enriched olive oils (one enriched with its own PC and another combined with thyme PC) increased IRH and plasma concentrations of retinol, β-cryptoxanthin and α-tocopherol, compared to a control virgin olive oil. A positive post-intervention correlation was observed for IRH values and HDL-c, β-cryptoxanthin, lutein and α-tocopherol. Results suggest that preservation of plasmatic fat-soluble vitamins by PC from FVOOS could partially explain the endothelial function benefits.