Abstract Background Recent studies have reported that prehypertension is associated with increased values of common carotid artery intima–media thickness (CCA-IMT). The aim of this study was to assess the impact of daytime ambulatory blood pressure (BP) levels on the association of prehypertension with CCA intima–media thickening in prehypertensive subjects. Methods A total of 807 subjects with office systolic BP < 140 and diastolic BP < 90 mmHg, underwent 24 h ambulatory BP (ABP) monitoring and carotid artery ultrasonographic measurements. The study population was divided into 3 groups according to office and daytime ABP levels: (1) normotensives: subjects with office BP < 120/80 mmHg and daytime ambulatory BP values within the normal range, (2) actual prehypertensives: individuals with office SBP (120–139 mmHg) and/or DBP (80–89 mmHg) and daytime ambulatory BP values within the normal range and (3) prehypertensives with masked hypertension (MH): patients with office SBP (120–139 mmHg) and/or DBP (80–89 mmHg) and elevated daytime ambulatory BP values. Results Prehypertensive patients with MH had higher ( p < 0.01) CCA-IMT values (0.712 mm; 95%CI: 0.698–0.725) than actual prehypertensives (0.649 mm; 95%CI: 0.641–0.656) and normotensives (0.655 mm; 95%CI: 0.641–0.670) even after adjustment for baseline characteristics. Normotensives and actual prehypertensives did not differ significantly regarding CCA-IMT values ( p > 0.05). After adjusting for potential confounders, (including demographic characteristics, vascular risk factors, and office BP) prehypertension with MH was independently ( p < 0.01) associated with a 0.06 mm increment in CCA-IMT (95%CI: 0.03–0.09). Conclusions Patients with office BP levels in the prehypertensive range, who also have elevated daytime ABP levels, had higher CCA-IMT values than patients with prehypertension with normal daytime ABP values and normotensive individuals.