Peritoneal dialysis (PD) or conventional hemodialysis (HD) are considered to be equally efficient dialysis methods in children and adolescents. The aim of our study was to analyze whether an intensified, nocturnal HD program (NHD) is superior to PD in an adolescent cohort. Thirteen patients were prospectively enrolled in a NHD program. We measured uremia-associated parameters, parameters for nutrition, medication and blood pressure and analyzed the data. These data were compared to those of 13 PD controls, matched for gender, age and weight at the beginning the respective dialysis program and after 6 months of treatment. Serum phosphate levels decreased significantly in the NHD group and remained unchanged in the PD group. Arterial blood pressure in the NHD was significantly lower despite the reduction of antihypertensive treatment, whereas blood pressure levels remained unchanged in the PD controls. Preexisting left ventricular hypertrophy resolved and albumin levels improved with NHD. Dietary restrictions could be lifted for those on NHD, whereas they remained in place for the patients on PD treatment. Residual diuresis remained unchanged after 6 months of either NHD or PD. NHD patients experienced fewer days of hospitalization than the PD controls. Based on our results, NHD results in significantly improved parameters of uremia and nutrition. If individually and logistically possible, NHD should be the treatment modality of preference for older children and adolescents.