Background Endothelial dysfunction may contribute to the pathophysiology of migraine with aura. Stromal cell‐derived factor‐1 alpha (SDF‐1α) is involved in the maintenance of endothelial integrity via mobilization of vascular stem cells. Objectives We sought to determine whether SDF‐1α levels are decreased in women with MA. Methods In this post hoc analysis of a case‐cohort study, levels of SDF‐1α were determined by enzyme‐linked immunosorbent assay. Endothelial function was assessed using peripheral arterial tonometry. Arterial stiffness was assessed by fingertip tonometry derived and heart‐rate‐adjusted augmentation index (AI). Results Twenty‐eight women with MA and 27 age‐matched healthy women were included in this study. Levels of SDF‐1α were significantly lower in women with MA compared to age‐ and risk factor‐matched healthy women (1763 ± 281 vs 2013 ± 263 pg/mL, P = 0.006). SDF‐1α levels were positively correlated with AI in healthy women ( r = 0.49, P = 0.009), but not in women with MA ( r = 0.05, P = 0.78). SDF‐1α levels were negatively correlated with CD144‐positive endothelial microparticles (EMP; r = −0.31, P = .02), and activated CD62E‐positive EMP ( r = −0.35, P = .01). Conclusion Levels of SDF‐1α are decreased in women with MA and are associated with EMPs as a surrogate marker of endothelial dysfunction. This might contribute to the pathophysiology and vascular risk in MA, but evidence from larger prospective studies is warranted.