Objectives We evaluated the association between cardiovascular risk factors and the magnitude of the difference in systolic blood pressure (SBP) between office and ambulatory measurements (masked effect) in untreated individuals without apparent hypertension-mediated organ damage (HMOD). Methods The inclusion criteria were 1) age ≥ 20 years, 2) blood pressure ≥ 140/90 mmHg at the outpatient clinic, and 3) not receiving antihypertensive medications. The difference between office and ambulatory SBP was calculated by subtracting the ambulatory daytime SBP from the office SBP. The association between the masked effect and SBP variability was analyzed in individuals without HMOD (no electrocardiographic left ventricular hypertrophy, spot urine albumin-to-creatinine ratio < 30 mg/g, and estimated glomerular filtration rate ≥ 60 mL/min/1.73 m2, n = 296). Results Among the cardiovascular risk factors, ambulatory BP variability was significantly correlated with the SBP difference. The standard deviation (SD) and coefficient of variation (cv) of 24-h SBP exhibited a significant negative linear association with the SBP difference in univariate and multivariate analyses adjusted for age, sex, presence of diabetes, and 24-h ambulatory SBP. A significant association was observed in patients with ambulatory daytime hypertension. In the multivariate analysis, individuals with a negative SBP difference > -5 mmHg exhibited a higher SD and cv of 24-h SBP than those with a negative SBP difference ≤ -5 mmHg or a positive SBP difference. Conclusions The results of our study suggest that the magnitude of the negative difference in office and ambulatory SBP may be a potential risk factor, even in individuals without apparent HMOD. Trial registration This trial is registered with ClinicalTrials.gov (NCT03855605).