Increased blood pressure (BP) variability is associated with the development of target organ damage. However, the optimal type and index of BP variability (BPV) regarding their prognostic significance is unclear. The aim of our study was to compare the association of ambulatory and home BPV with the left ventricular mass index (LVMI) in patients with chronic kidney disease (CKD). From a total of 1560 consecutive subjects, 137 hypertensive patients with CKD underwent home and ambulatory BP monitoring and echocardiographic measurements. The variability of home BP monitoring was quantified by using the standard deviation (SD), coefficient of variation (CV), and morning minus evening BP values. Ambulatory BPV was quantified using the SD, CV, and the time rate (TR) of BP variation. The univariate analysis demonstrated that day-to-day systolic SD and the 24-h TR of systolic BP (SBP) variation were significantly associated with the LVMI. The multivariate linear regression analysis showed a significant and independent association of the LVMI with the 24-h TR of SBP variation (B = 9.204, 95% CI: 1.735-16.672; p = 0.016). A 0.1-mmHg/min increase in the 24-h TR of SBP variation was associated with an increment of 9.204 g/m in the LVMI, even after adjustment for BP and other vascular risk factors. In conclusion, ambulatory BPV but not home BPV was associated with the LVMI in CKD patients. The 24-h TR of SBP variation was the only BPV index associated with the LVMI, independent of average BP values.