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.