Aim: To compare the measurement of total body water (TBW) and fat-free mass (FFM) using the criterion method of deuterium dilution space (2H2O) with bioelectrical impedance analysis (BIA) using a portable QuadScan 4000, Bodystat® in children and adolescents with phenylketonuria (PKU). Methods: Sixteen patients with PKU, median age is 12.5 (range 5–20.6) years, were recruited into this cross-sectional study. TBW was measured by both deuterium dilution and BIA on the same occasion as per a standard protocol. FFM was estimated from predictive equations. Results: There was no significant difference between TBWDeut and TBWBIA (p = 0.344) or FFMDeut and FFMBIA (p = 0.111). TBWDeut and TBWBIA were highly correlated (r = 0.990, p < 0.0001), as were FFMDeut and FFMBIA (r = 0.984, p < 0.0001). Bland-Altman plots demonstrated that there was no proportional bias between the criterion method, TBWDeut, and the test method TBWBIA, in estimating TBW (β = −0.056, adjusted r2 = 0.069, p = 0.169) or FFM (β = −0.089, adjusted r2 = 0.142, p = 0.083). Conclusion: Our results suggest that when compared with the criterion method, the QuadScan 4000, Bodystat® can reliably be used to predict TBW and FFM in patients with PKU. We suggest that due to the portability and non-invasive approach, this method can reliably be used to monitor body composition in the outpatient clinic setting, to further improve the monitoring and assessment of nutritional status in PKU.