Objectives: Statin use during hospitalization improves prognosis in patients with ischaemic stroke. However, it remains uncertain whether acute ischaemic stroke patients with chronic kidney disease (CKD) benefit from statin therapy. We investigated the effect of statin use during hospitalization in reducing short-term mortality of patients with ischaemic stroke and CKD. Methods: Data of first-ever ischaemic stroke patients without a history of pre-stroke statin treatment was derived from the China National Stroke Registry. Patients were stratified according to estimated glomerular filtration rate (eGFR): normal renal function (eGFR ≥90 mL/min/1.73 m2), mild CKD (eGFR 60–90 mL/min/1.73 m2) and moderate CKD (eGFR < 60 mL/min/1.73 m2). Multivariate logistic regression analysis was used to evaluate the association between statin use during hospitalization and all-cause mortality with different renal functions at 3-month follow-up. Results: Among 5,951 patients included, 2,595 (43.6%) patients were on statin use during hospitalization after stroke (45.7% in patients with normal renal function, 42.0% in patients with mild CKD, and 39.0% in patients with moderate CKD). Compared with the non-statin group, statin use during hospitalization was associated with decreased all-cause mortality in patients with normal renal function (OR 0.65, 95% CI 0.43–0.97, p = 0.04), mild CKD (OR 0.59, 95% CI 0.38–0.91, p = 0.02) and moderate CKD (OR 0.41, 95% CI 0.23–0.75, p = 0.004) at 3-month follow-up. Conclusions: Statin use during hospitalization was associated with decreased 3-month mortality of ischaemic stroke patients with mild and moderate CKD. However, the conclusion should be confirmed in further studies with larger population, especially with moderate CKD.