Although serum uric acid (UA) has been reported to be positively associated with increased arterial stiffness as evaluated by cardio-ankle vascular index (CAVI), UA also has an antioxidative effect that prevents endothelial damage. Therefore, the status of endothelial repair induced by endothelial damage might affect the correlation between UA and CAVI. To clarify the correlation between UA and CAVI in relation to endothelial repair activity, we performed a cross-sectional study with 246 Japanese men aged 60–69 years undergoing a general health check-up. The analysis was stratified by the median circulating level of CD34-positive cells because circulating levels of CD34-positive cells could indicate the degree of endothelial repair activity. Independent of known cardiovascular risk factors, among participants with high circulating levels of CD34-positive cells (0.95 cells/μL ≤), UA was significantly positively correlated with CAVI (standardized parameter estimate β = 0.23, p = 0.009), but not among participants with low circulating levels of CD34-positive cells (< 0.95 cells/μL) (β = 0.07, p = 0.445). Independent of established cardiovascular risk factors, UA levels were significantly positively correlated with increased arterial stiffness only among participants with aggressive endothelial repair as evaluated by circulating levels of CD34-positive cells. These results might help clarify some background mechanisms related to endothelial activity.