Our study aimed to evaluate factors affecting circadian BP profile and its association with hypertension-mediated organ damage (HMOD) in pediatric patients with primary hypertension (PH). The study included 112 children (14.7 ± 2.1 age, 79 boys, 33 girls) with untreated PH. Non-dipping was defined as a nocturnal drop in systolic or diastolic BP (SBP, DBP) < 10%, and a nocturnal drop >20% was defined as extreme dipping. The nocturnal SBP drop was 10.9 ± 5.9 (%), and the DBP drop was 16.2 ± 8.5 (%). Non-dipping was found in 50 (44.6%) children and extreme dipping in 29 (25.9%) patients. The nocturnal SBP decrease correlated with BMI Z-score (r = −0.242, p = 0.010) and left ventricular mass index (LVMI) (r = −0.395, p = 0.006); diastolic DBP decrease correlated with augmentation index (AIx75HR) (r = 0.367, p = 0.003). Patients with a disturbed blood pressure profile had the highest LVMI (p = 0.049), while extreme dippers had the highest augmentation index (AIx75HR) (p = 0.027). Elevated systolic and diastolic BP dipping were risk factors for positive AIx75HR (OR 1.122 95CI (1.009–1.249) and OR 1.095 95CI (1.017–1.177). We concluded that disturbed circadian BP profile was common in children with PH and should not be considered a marker of secondary hypertension. A disturbed circadian BP profile may be associated with higher body weight. In pediatric patients with PH, non-dipping is associated with increased left ventricular mass, and extreme dipping may be a risk factor for increased arterial stiffness.