The evaluation of fat-free mass (FFM) in patients with Duchenne muscular dystrophy (DMD) is useful to investigate disease progression and therapeutic efficacy. This study aimed to validate the Bioelectrical impedance (BIA) method compared with the dual-energy X-ray absorptiometry (DXA) for estimating the %FFM in boys with DMD. This is a cross-sectional study performed with children and adolescents diagnosed with DMD. Resistance and reactance were measured with a BIA analyzer, from which eight predictive equations estimated the %FFM. The %FFM was also determined by DXA and its used as a reference method. Pearson correlation test, coefficient of determination, the root-mean-square error, the interclass correlation coefficient, and linear regression analysis were performed between %FFM values obtained by BIA and DXA. The agreement between these values was verified with the Bland-Altman plot analysis. Forty-six boys aged from 5 to 20 years were enrolled in the study. All the equations showed a correlation between the %FFM estimated by BIA and determined by DXA (p < 0.05). The Bland-Altman method indicated that two equations have a significant bias (p < 0.05) and six equations showed no significant bias of %FFM (p > 0.05). However, one of them has high variation and wide limits of agreement. Five of eight %FFM predictive equations tested in DMD were accurate when compared with the DXA. It can be concluded that BIA is a validity method to evaluate patients with DMD.