Introduction: Vascular calcification, linked to atherosclerosis, is a significant cardiovascular risk factor in chronic kidney disease (CKD). While different intracranial carotid arteriosclerosis subtypes affect stroke risk in the general population, their prevalence, causes, and impact on CKD patients remain unclear. Methods: This cohort study used data from the National Taiwan University Hospital’s pre-end-stage renal disease care database, including 2,622 CKD patients with brain CT scans from 2006 to 2020. Intracranial carotid artery calcifications were categorized as intimal or internal elastic lamina (IEL) subtypes. Multivariable Cox regression assessed the associations between each calcification subtype and incident stroke or vascular mortality. Results: Among 2,622 patients, 2,470 (94.2%) had calcifications classifiable as intimal (n = 719, 27.4%), IEL (n = 1,642, 62.6%), or mixed (n = 109, 4.2%) subtypes. Multivariable analysis revealed that IEL subtype was associated with older age, diabetes, prior vascular diseases, and impaired renal function (p < 0.05). Over a median follow-up of 3.9 years, IEL subtype exhibited a higher risk of any stroke (adjusted hazard ratio [HR] [95% CI]: 2.0 [1.2–3.2], p = 0.007) and vascular death (adjusted HR [95% CI]: 2.0 [1.4–3.0], p < 0.001), compared to those without calcification. Furthermore, the IEL subtype displayed a higher risk of any stroke (adjusted HR [95% CI]: 1.6 [1.1–2.3], p = 0.017) and vascular death (adjusted HR [95% CI]: 1.6 [1.3–2.1], p < 0.001) compared to the intimal subtype. Conclusion: IEL calcification is prevalent in CKD patients and associated with aging, diabetes, and impaired renal function. It poses a higher risk of cerebrovascular events compared to those without calcification or with intimal calcification.