Background: This prospective cohort study compared the changes in body water composition and nutritional parameters measured with multifrequency bioimpedance analysis between 8-hour three times weekly nocturnal hemodialysis (NHD) and 4-hour conventional hemodialysis (CHD) patients. Patients and Methods: 55 patients on CHD and 57 patients on NHD were included in the study. Multifrequency bioimpedance analysis was performed at baseline and at the 12th month. The primary outcomes of the study were changes in extracellular water (ECW), fat mass, dry lean mass and phase angle. Secondary outcomes of the study included changes in blood pressure and biochemical parameters related to nutrition and inflammation. Results: ECW/height values decreased in the NHD group, while they increased in the CHD group. Fat mass, dry lean mass, and serum albumin increased and high sensitive CRP decreased in the NHD group but did not change in the CHD group. When changes in parameters from baseline to the 12th month between the groups were compared, NHD was associated with improvement in volume parameter including ECW/height (difference -0.44 l/m, p < 0.001). Change in blood pressure was not different between the groups, however requirement for antihypertensive medication decreased from 26.5 to 8.5% in the NHD group (p = 0.002). NHD was also associated with increases in fat mass (difference 1.8 kg, p < 0.001), dry lean mass (difference 0.6 kg, p = 0.006), serum albumin (difference 0.19 g/dl, p < 0.001) and cholesterol (difference 18.8 mg, p < 0.001). Phase angle values decreased in the CHD group but did not change in the NHD group (difference between the groups 0.37°, p = 0.04). Conclusion: This study revealed that longer HD facilitates volume control and improves nutritional status.