The peak width of skeletonized mean diffusivity (PSMD) is a novel marker for white matter damage related to small vessel disease. The aim of this study was to investigate the white matter damage related to small vessel disease in patients with early chronic kidney disease (CKD) using PSMD. We prospectively enrolled 18 patients with early CKD, and also included age and sex-matched 18 healthy controls. Diffusion tensor imaging (DTI) was performed using the three tesla MRI scanner in participants. We obtained the PSMD based on the DTI by several steps including preprocessing, skeletonization, application of a custom mask, and histogram analysis. The patients with CKD were also performed a neuropsychological test. We compared the PSMD between the groups, and also performed correlation analysis between PSMD and clinical data. There was significant difference of the PSMD between the patients with CKD and healthy controls. The PSMD was higher in the patients with CKD than that in the healthy control group (2.652±0.500 vs. 2.301±0.256 ×10-4 mm2/s, p<0.001). In addition, the PSMD was positively correlated with age in patients with CKD and healthy controls (r=0.525, p=0.025; r=0.672, p=0.002; respectively). The PSMD was also correlated with verbal fluency test and trail-making test (r=-0.579, p=0.012; r=0.849, p<0.001; respectively). PSMD is a valuable marker for detecting white matter damage related to small vessel disease in patients with CKD. Our study indicates more extensive white matter damage in patients with early CKD compared to healthy controls, and it correlates with frontal lobe-related cognitive impairment. It underscores its potential role in assessing both structural and functional brain changes in this population.