The study examined the association between estimated glomerular filtration rate (eGFR) and large cerebral artery stenosis (LCAS) in 1011 asymptomatic South Korean adults aged 45 years and older with cardiovascular risk factors. LCAS was defined as stenosis ≥50% or occlusion of intracranial or extracranial cerebral arteries, assessed by magnetic resonance angiography (MRA). eGFR was calculated according to the CKD-EPI 2009 equation based on creatinine. Higher eGFR values were independently associated with a lower risk of LCAS; each increase in eGFR of 1 mL/min/1.73 m² reduced the risk by 1% (OR = 0.99, 95% CI: 0.98–1.00). The highest eGFR tertile (T3) had a 39% lower risk of LCAS compared to the lowest (T1) (OR = 0.61, 95% CI: 0.39–0.96). The association was significant in women (OR = 0.98, 95% CI: 0.96–0.99; P = 0.009) and statin users (OR = 0.97, 95% CI: 0.95–0.99; P = 0.015), but the interactions were not statistically significant. The findings require confirmation in prospective studies and other populations.