Athletic amenorrhea has been associated with endothelial dysfunction and unfavorable lipid profile. Estrogen substitution may reverse these metabolic consequences. The aim of this study was to evaluate the effects of oral contraceptives (OCs) on endothelial function measured as flow-mediated dilatation (FMD) of the brachial artery, the lipid profile and blood markers of endothelial activation (inflammation) in amenorrheic athletes. Age- and BMI-matched groups of young endurance athletes with amenorrhea (n = 11), regularly cycling athletes (n = 13), and sedentary controls (n = 12) were examined before and after 9 months of treatment with a low-dose monophasic, combined OC (30 µg ethinyl estradiol + 150 µg levonorgestrel). The amenorrheic athletes displayed the lowest FMD at baseline and the largest increase after OC treatment. FMD also increased in the control group, but not in the regularly menstruating athletes who had the highest values of FMD before treatment. All three groups, and particularly the controls showed moderate unfavorable changes in the lipid profile in accordance with previous known effects of a second-generation OC. Furthermore, there was an overall increase in some inflammatory markers (high sensitive-CRP and tissue necrosis factor ) and a decrease in one of the markers (vascular cell adhesion molecule-1). We conclude that amenorrheic athletes benefit from treatment with OC with respect to endothelial function. OC treatment is also associated with some modest alterations in the lipid profile and in markers of inflammation.