In estrogen‐deficient post‐menopausal women, osteoporosis shares a common link with cardiovascular disease risk, including endothelial dysfunction. The current study sought to examine associations between bone mineral density (BMD) and endothelial function in estrogen‐deficient premenopausal women with exercise‐associated menstrual disturbances. Recreationally trained women (24.3 ± 0.8 years; overall mean ± SEM) who were estrogen deficient (amenorrheic or eumenorrheic anovulatory cycles; E2Def; n = 13) or estrogen replete (eumenorrheic ovulatory cycles; E2Rep; n = 14) were studied. Total body and lumbar BMD (L1‐L4) were determined using dual‐energy X‐ray absorptiometry. Serum markers of oxidative stress (oxidized low‐density lipoprotein; OxLDL), energy deficiency (triiodothyronine), and bone turnover (osteocalcin, c‐telopeptide X, P1NP) were assessed. Estrogen exposure was determined by assessing daily urinary estrone‐3‐glucuronide (E1G) across a monitoring period. Calf blood flow (CBF), an index of endothelial function, was measured using strain‐gauge plethysmography. CBF, total body and L1‐L4 BMD, triiodothyronine and E1G were lower (P < 0.05), and c‐telopeptide crosslinks higher (P < 0.05) in E2Def. Osteocalcin and OxLDL did not differ (P > 0.05) between groups. L1‐L4 BMD, osteocalcin, and E1G were the strongest predictors of CBF (R2=0.615, P < 0.001). CBF was the strongest predictor of L1‐L4 BMD (R2=0.478, P < 0.001). L1‐L4 (r = 0.558, P = 0.008) and CBF (r = 0.534, P = 0.004) were independently correlated with E1G. In young recreationally trained premenopausal women with anovulatory menstrual disturbances, low CBF predicts decreased lumbar BMD, suggesting impaired peripheral endothelial function may predict early unfavorable changes in bone metabolism. This finding may be of relevance in the early detection of cardiovascular and bone health decrements in otherwise healthy estrogen‐deficient premenopausal women.