Background: Studies show inconsistent results regarding the relationship between Helicobacter pylori (H. pylori) infection and stroke. The present study assessed a potential association between H. pylori infection and an important risk factor for stroke, intracranial atherosclerosis.Methods: In total, 15,798 subjects with transcranial Doppler (TCD) and 13C-urea breath test (13C-UBT) were enrolled from March 2012 to March 2017. Intracranial atherosclerosis was further measured using intracranial carotid artery calcification (ICAC) on past or recent head CT, and 14,084 subjects were ultimately included in the study. Baseline demographics, atherosclerosis risk factors, and laboratory results were investigated. Since endothelial dysfunction is critical to the development of atherosclerosis, the role of H. pylori in migration, tube formation, and proliferation of human brain microvascular endothelial cells (HBMECs) was assessed in vitro.Results: The intracranial atherosclerosis group had a higher proportion of women and a greater rate of H. pylori infection than those without intracranial atherosclerosis. H. pylori infection was significantly more common in women with intracranial atherosclerosis than males. In addition, the incidence of intracranial atherosclerosis was significantly higher in women with H. pylori infection than uninfected women (53.8 vs. 46.4%, p < 0.001). In an adjusted model, H. pylori was shown to be an independent risk factor for intracranial atherosclerosis in women ≤ 60 years of age [odds ratio (OR) = 2.261, 95% CI = 1.839–2.780, p < 0.001]. Serum exosomes from patients with H. pylori infection had significantly reduced brain endothelial cell migration, tube formation, and proliferation in vitro.Conclusion:Helicobacter pylori infection may be an important independent risk factor for intracranial atherosclerosis in women ≤ 60 years of age.