Chronic kidney disease has been linked to cognitive impairment and morphological brain change. However, less is known about the impact of kidney functions on cerebral cortical thickness. This study investigated the relationship between kidney functions and global or lobar cerebral cortical thickness (CTh) in 259 non-demented elderly persons. Forty-three participants (16.7%) had kidney dysfunction, which was defined as either a glomerular filtration rate (GFR) of <60 ml/min/1.73 m2 or presence of proteinuria. Kidney dysfunction was associated with lower global (β = -0.05, 95% CI = -0.08 to -0.01) as well as frontal, parietal, temporal, occipital, and insular lobar CTh. In the stratified analysis, the associations were more pronounced in women, APOEε4 non-carriers, and participants with a lower cognitive score. Besides, kidney dysfunction significantly increased the risk of cortical thinning, defined as being the lowest CTh tertile, in the insular lobe (adjusted odds ratio = 2.74, 95% CI = 1.31-5.74). Our results suggested that kidney dysfunction should be closely monitored and managed in elderly population to prevent neurodegeneration.